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`IPR2017-01374
`Genentech Exhibit 2001
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` MICROFILMED
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`To maintain document/film
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`Genentech Laboratory Notebook Procedures
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`4)
`Use dark permanentink to record all of your work in your notebook on a daily basis. Sign and date
`each day’s entries.
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`2)
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`Ty
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`<rRRRRARESETTSPTee
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`DN
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`SCIENTIFIC NOTEBOOK CO.
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`ee———E—————
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`Page 12 of 90
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`Page 12 of 90
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`

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`Page 13 of 90
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`Page 13 of 90
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`

`

`Project No.
`Book No.
`
`
`
`From Page No.__
`
`[f-2s
`34-37
`
`|
`
`Ame
`
`5 9-63
`Sb-bo
`70-73
`67-70
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`0. Ps4
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`Uding 1FAT as Complete,
`LAT vs 1FBY pp .b23A
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`|
`
`To Page No.___
`
`Page 14 of 90
`
`Page 14 of 90
`
`

`

`64 template TITLE (hvurage Corrs
`
`Project No
`Book No
`
`From Page No.__
`
`BRK ARERR ER RARER RE RH RRR KERR IR ERE RRR NI RE RIK KIRK RIK TIN INR RRR RD
`Ga:::: letters ~ Ca < 1.0A from 1FB4 HV
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`iFB4 and 3FAB are lambda-type
`2MCP, 1FBJ AND 2HFL are kappa-type
`+
`a-strand residues
`() denotes be
`
`Witnessed & Understood by me,
`
`To Page No.
`
`Invented by
`
`Page 15 of 90
`
`Page 15 of 90
`
`
`

`

`4
`
`Project No._._
`Book No. TITLE
`
`(]
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`L&#.
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`GAP IN SEQUENCE:
`O-
`3 in file: 1FB4.PDBASALA
`GAP IN SEQUENCE:
`8-
`17 in file: 1FB4.PDBASALA
`GAP IN SBQUENCE:
`23-
`33 in file:1FB4.PDBASALA
`GAP IN SEQUENCE:
`4i-
`45 in file: 1F54.PDBASALA
`GAP IN SEQUENCE:
`51i-
`58 in file:1FB4.?DBASALA
`GAP IN SEQUENCE:
`62-
`67 in file:1FB4.PDBASALA
`GAP IN SEQUENCE:
`72-
`76 in file: 1FPB4.PDBASALA
`GAP IN SEQUENCE:
`B3-
`92 in file:1FB4.PDBASALA
`GAP IN SEQUENCE:
`98- 107 in file: 1FB4.PDBASALA
`1PBJ.PDBASALA
`62 residues and
`GAP IN SEQUENCE:
`o-
`3
`in file:1FBJ.PDBASALA
`GAP IN SEQUENCE:
`17 in file:1FBJ.PDBASALA
`8-
`GAP IN SEQUENCE:
`23-
`33 in file:1FBJ.PDBASALA
`GAP IN SEQUENCE:
`4i-
`45 in file: 1FBJ.PDBASALA
`51-
`58 in file:1FBJ.PDBASALA
`GAP IN SEQUENCE:
`62-
`67 in file: 1FBJ.PDBASALA
`72-
`76 in file: 1FBJ.PDBASALA
`GAP IN SEQUENCE:
`GAP IN SEQUENCE:
`83-
`92 in file:1PBJ.PDBASALA
`GAP IN SEQUENCE:
`98- 107 in file: 1FBJ.PDBASALA
`2HFL. PDBASALA
`62 residues and
`GAP IN SEQUENCE:
`o=
`3 in file: 2HFL.PDBASALA
`GAP IN SEQUENCE:
`17 in file: 2HFL.PDBASALA
`8-
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`23-
`33 in file: 2HFL.PDBASALA
`GAP IN SEQUENCE:
`4l1-
`45 in file: 2HFL.PDBASALA
`GAP IN SEQUENCE:
`51-
`58 in file: 2HFL.PDBASALA
`GAP IN SEQUENCE:
`62~
`67 in file: 2HFL.PDBASALA
`GAP IN SEQUENCE:
`72-
`76 in file: 2HFL.PDBASALA
`(GAP IN SEQUENCE:
`83-
`92 in file: 2HPL.PDBASALA
`GAP IN SEQUENCE:
`98- 105 in file: 2HFL.PDBASALA
`2MCP. PDBASALA
`62 residues and
`(GAP IN SEQUENCE:
`o-
`3 in file: 2MCP.PDBASALA
`GAP IN SEQUENCE:
`17 in file: 2MCP.PDBASALA
`8-
`GAP IN SEQUENCE:
`23-
`33 in file: 2MCP,.PDBASALA
`GAP IN SEQUENCE:
`4l-
`45 in file: 2MCP.PDBASALA
`GAP IN SEQUENCE:
`51-
`60 in file: 2MCP.PDBASALA
`' GAP IN SEQUENCE:
`64-
`69 in file: 2MCP.PDBASALA
`GAP IN SEQUENCE:
`74-
`78 in file:
`2MCP.PDBASALA
`~ GAP IN SEQUENCE:
`85-
`94 in file: 2MCP.PDBASALA
`GAP IN SEQUENCE:
`100- 111 in file: 2MCP.PDBASALA
`3FAB. PDBASALA
`62 residues and
`GAP IN SEQUENCE:
`O0-
`3
`in f£ile:3FAB.PDBASALA
`GAP IN SEQUENCE:
`8-
`17 in file:3FAB.PDBASALA
`= GAP IN SEQUENCE:
`23-
`33 in file: 3FAB.PDBASALA
`GAP IN SEQUENCE:
`41-
`45 in file: 3FAB.PDBASALA
`_ GAP IN SEQUENCE:
`51-
`57 in file:3FAB.PDBASALA
`GAP IN SEQUENCE:
`61-
`66 in file:3PAB.PDBASALA
`GAP IN SEQUENCE:
`71-
`75 in file:3FAB.PDBASALA
`GAP IN SEQUENCE:
`82-
`91 in file: 3PAB.PDBASALA
`GAP IN SEQUENCE:
`97- 108 in file:3FAB.PDBASALA
`_ GAP IN SEQUENCE:
`108- 107 in file:3FAB.PDBASALA
`MAXAT =
`306 : MAXRES =
`62
`B-factor range is:
`2,00 ta 33.72
`~ B-factor BIN range is: Zt
`34
`B-FACTOR STATS DO NOT INCLUDE 3PAB
`Dist range
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`Range
`Avg.Dst. R.M.S. values
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`0.391
`0.455
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`eee hp
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`|ssNeCa Ca-C C=O C-N Ca-Cb C-N-Ca N-Ca-C Ca-C=0 Ca-C-N O-C-N N-Ca- m4
`1.451 1.507 1.160 1.282 1.499
`125.3
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`
`Page 16 of 90
`
`Page 16 of 90
`
`

`

`i)
`
`c
`
`CQHEL ,
`
`p » Project No.
`
`Book No.______
`
`
`
`5
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`Gut Ks
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`PT |[Senet
`tn, AHFL anattade % LFBY
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`ek teeRee eR TR TA RRA REE RE EATER EKER
`1FB4 and 3FAB are lambda-type
`2MCP, 1FBJ AND 2HFL are kappa-type
`
`capital letters = Ca < 1.0A from 2HFL HV
`
`
`
`KK KEKE KKK RRR EEEKRE KER RARER ERE EERE ER KEKE EERE EAREREEAKREREERERE 1.+re ee: +.=" s -
`
` () denotes beta-strand residues
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`Te Compare thy tuo anerage wtrietinea) ute MCs C
`fh Aes: 3-b,14-23, 33-4, #55), SE42, F-71, 26-43, (24%,
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`C=O C-N Ca-Cb C-N-Ca N-Ca-C Ca-C-0 Ca-C-N O-C-N N-Ca-Cb Cb-Ca-C
`L006 1.525 1.202 1.293. 1.6501
`124.6
`199.7
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`
`Page 17 of 90
`
`Page 17 of 90
`
`

`

`Project No.
`Book No.
`
`
`
`aa
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`1FBJ AND 2HFL are kappa-type
`1FB4 and 3FAB are lambda-type
`2MCP,
`{) denotes beta-strand residues
`capital letters = Ca < 1.0A from 1FB4 HV
`"Sequences of Proteins of Immunological
`consensus sequence from Kabat et al.,
`‘
`4th ed.
`1987; nun
`Interest",
`cording to Kabat;
`mbering ac
`* marks Kabat variance between 1 ~ 10,
`@ variance between 11 - 20
`RRC RC RII RR OR OR RT IR RT RR AIOE RR RII RTI RE IRR ER ERIE RARER
`
`Witnessed & Understood by me
`
`DreeeVeAasvomxaHePye
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`By3GyPai,OEYOLCOGeANNOH*
`
`To Page No.
`
`Page 18 of 90
`
`Page 18 of 90
`
`

`

`2HFL
`1000.0
`-93.
`129.8 -164.
`—122.
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`Page 19 of 90
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`Page 20 of 90
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`

`

`Witnessed & Understood by me,
`
`Bond Lengths & Angles for AVERAGE after 200 cycles minimization (.COR3)
`N-Ca Ca-C C0 C-N Ca-Cb C-N-Ca N-Ca-C Ca-C=0 Ca-C-N O=C-N N-Ca-Cb
`1.454 1.526 1.230 1.337 1.530 124.2
`109.7
`220.2
`116.6
`123.3
`109.6
`0.003 0.003 0.002 0.002 0.001
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`1.4
`0.6
`0.8
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`0.6
`64
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`55
`60
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`64
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`55.
`60
`Bond Lengths & Angles for AVERAGE
`(.COR4)
`after 300 cycles minimization (100 Ca released)
`H-Ca Ca-C
`C*O C-N Ca-Cb C-N-Ca N-Ca-C Ca-C=0 Ca~C-N O=C-N
`1.454 1.528 1.231 1.338 1.531 124.2
`109.9
`120.4 Mie.8,
`872.2
`0,002 0.002 0.001 0.001 9.001
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`55
`55
`Bond Lengths 4 Angles for AVERAGE
`(.COR5)
`after 600 cycles minimization (400 Ca released)
`N-Ca Ca-C
`CeO C-N Ca-Cb C-N-Ca N-Ca-C Ca-C=0 Ca-C-N O=C-N
`1,454 1.528 1.230 1.338 1.531 124.1
`110.0
`120.5
`116.5
`123.1
`6.002 0.002 0.001 0.001 0.001
`0.6
`0.8
`0.4
`0.4
`0.2
`64
`64
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`Project No.
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`Page 21 of 90
`
`Bond Lengths & Angles for HVONFB4HV
`N-Ca Ca-C
`CQ C-N Ca-Cb C-N-Ca N-Ca~C Ca-C=0 Ca-C-N O=C-N N-Ca-Cb
`1.451 1.507 1.160 1.282 1.499
`125.3
`110.3
`120.9
`117.6
`122.2
`110.6
`0.023 0.033 0.177 0.065 0.039
`4.6
`2.8
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`2.5
`62
`62
`62
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`58
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`62
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`Bond Lengths 4 Angles for AVERAGE after 50 cycles minimization (.COR)
`wa Ca-C
`C*O C-N Ca-Cb C-N-Ca N-Ca-C Ca-C=0 Ca~-C-N O=C-N N-Ca-Cb
`1.450 1.522 1.230 1.334 1.528 123.6
`109.4
`120.1
`116.6
`123.3
`109.8
`0.005 0.006 0.002 0.005 0.003
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`Bond Lengths & Angles for AVERAGE after 100 cycles minimization (.COR2)
`N-Ca Ca-C
`C=0 C-N Ca-Cb C-N-Ca N-Ca-C Ca-C=0 Ca-C-N O=C-N N-Ca-Cb
`0.453 1.524 1.232 1.335 2.530 124.0
`108.5
`120.1 ELé.8
`123.9
`109.8
`0.004 0.005 0.003 0.004 0.002
`1.1
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`Bond Lengths & Angles for AVERAGE after 200 cycles minimization with Ca
`{(.COR3¢)
`50 cycles with Ca at 10
`100 cycles with Ca at 2.5
`100 cycles with Ca at 0.5
`C=O C-N Ca-Cb C-N-Ca N-Ca-C Ca-C=0 Ca-C-N O=C-N N-Ca-Cb
`N-Ca Ca-c
`1.455 1.528 1.231 1.338 1.531 124.2
`110.0
`130.4 LI6.5
`123.2
`109.5
`©.002 0.002 0.001 0.001 0.001
`0.6
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`0.4
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`himimneraheow 9 Book No.__
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`
`
`TITLE
`
`Page 21 of 90
`
`

`

`CeeeT
`Project No.
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`10
`Book No...———s—<—Ssé«‘i*'TTLLE
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`From Page No.
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`Dihedral
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`les for AVERAGE after 600 cycles minimization
`1
`les for AVERAGE after 200 cycles minimization
`PHI
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`1000.0
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`39 =204.7
`99.0
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`58.8
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`S38
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`184.5
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`174.2
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`129.9
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`265.39 175.6
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`Witnessed & Understood by me,
`
`Date
`
`Date
`
`To Page No. IG
`
`Recorded by
`
`Page 22 of 90
`
`Page 22 of 90
`
`

`

`
`Project No._____
`Book No.
`
`
`
`riTLE
`From Page No. [0
`
`11
`
`h Ca at 20.0
`
`ee
`
`fpr
`
`4
`
`=
`
`Dihedral Angles for AVERAGE
`after 200 cycles minimization wit
`50 cycles with Ca at 10.0
`100 cycles with Ca at 2.8
`»COR3C
`100 cycles with Ca at o. 5
`OMEGA
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`PHI
`179.8
`161.
`1000.0
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`174.4
`102.
`-96.6
`AVERAGE. PDBS
`AVERAGE . PDB3
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`146.
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`2.98
`98.0 132.8
`32.3-148.2
`6
`4
`1000.
`1000.0
`69.6
`118.7
`6.4
`40.7
`2.86
`149.3 108.9 -18.2
`33.3
`176.3
`168.
`a
`23
`3.00
`156.5
`1000.0
`179.5 =h.0
`3.0% 227.3 117,59 -10.6 THe
`73.3
`17722
`164.
`23
`5
`2.98
`142.8
`-118.7
`128.1
`20.0
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`2.69
`139.9 115.6
`17.3 -<So.8
`7
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`147.3
`~1 78.7
`157.
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`192,8
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`“61.4
`2.94
`131.0 11)...
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`175.4
`21
`7
`2.90
`154.0
`91.
`-133.6
`L32.3
`-5.8
`-41.4
`3.01
`152.5.123.8
`2.5
`28.3
`178.6
`142.
`=74.5
`18
`83
`3.2h 145.0
`13..
`-2.5
`-80.2
`2.84
`149.1 107.5 -28.5 -95.4
`=LTS.9
`83
`18
`2.90
`160.6
`156.
`116.6
`133.1 ~11.6
`61.3
`3.98
`199.9 113.2 -21.9 Fie
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`20
`81
`3.04
`142.1
`97.
`-146.0
`123.5
`8.2
`-49.3
`2.98
`134.2124.7
`3.9 “TH.2
`81
`20
`2.65
`153.6
`1000.
`1000.0
`=—2.2
`112.4
`29.5
`30.3
`2-89
`136.9 119.6
`18.7 80,2
`177.2
`22 7 2.76
`166.2
`130.
`1000.0
`iz2.9 8.9
`50.0
`2.91
`429.3 126.2 -22.6 Te
`79
`22
`3.00
`143.1
`144.
`178.5
`—99.5
`123.2 3.5
`42.9
`2.84
`152.8 110.6 -31.1 “BLS
`34
`52
`2.97
`164.4
`148.
`176.9
`=Laz.a
`126.7
`ce
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`2.95
`2145.0 128.7
`0.0 -57.8
`pa
`34
`2.95
`166.3
`178.8
`131.
`~1270..6
`120.6
`2.4
`72.0
`2.82
`134.7 [09.6
`L.7 “ae
`179.6
`35
`97
`2.89
`147.7
`138.
`=iLs.4
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`2.92
`136.0 116.7
`17.7 =.8
`97
`35
`a.85
`143.6
`176.4
`144.
`=~107..7
`123.7
`1.5
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`2.93
`158.2 2108.3
`25.4-102.4
`179.8
`36
`49
`2.54
`152.7
`105.
`~197..4
`3-
`162.0
`~-0.
`154.2
`2.90
`133,8 108.1 -14.3-i37.7
`179.0
`48
`36
`2.89
`156.1
`164.
`-70.0
`133,7 -10.9
`“$3.
`3.25
`136.8 175.6
`-3.2 ~Ee.T
`49
`36
`3.31
`143.8
`1000.0
`65.7
`1000.
`121.0 -15.8
`=49.0
`2,94
`149.5 113.5
`13.8
`80.9
`~ifs.3
`rH
`95
`2.96
`159.4
`isi.
`1000,0
`113,0 -15.6
`-88.0
`2.82
`166.3 103.6 -17.8 101.3
`95
`37
`2.85
`166.5
`177.8
`iid.
`-140.5
`{LT .6
`6.1
`68.3
`2.87
`155,1 120.9 -16.1 65.5
`38
`46
`2.87
`150.9
`=173..6
`123.
`“62.7
`111.0
`12.8
`15.9
`2.97
`245,9 112.2 L7.9 Ba
`46
`38
`2.64
`170.9
`~31.
`—L79.9
`~86..7
`123.8
`25.2
`a¢.2
`3.02
`134.0 118.3
`2.6 2.8
`39
`93 2. 153.7
`~173..4
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`123.4 —5.4
`77.8
`2.93
`130.3 117.5 -11.0 72.8
`93
`39
`3.123
`126.4
`=L7¥.4
`162.
`—156.7
`3.34
`102.1 123.9
`68.6~-159.8
`48
`46
`1000.0
`—157.5
`1k. 7° Ts.3
`-§5.9
`2.99
`141.7 121.4
`1.6-103.9
`61
`48
`a.7a
`170.0
`i78.3
`1000.0
`128.4
`8.6
`~178:.6
`-23.5 oe 134.2 127.3
`0.9 =ORLT
`—142.9
`127.2
`6.3
`50 a i 164.3
`59
`50
`3.13@ 148.6
`60.3
`2.91¢@ 148.5 118.8
`12.0 -69.7
`177.9
`~146.6
`3.05
`88.1 140.3
`11.6-139.0
`69
`67
`~178.4
`=76.5
`3,09
`200.0 135.2
`37.7-ERG.@
`70
`68
`1000.0
`-66.1
`2.92
`145.9 108.3 -27.0 79,8 ~
`69
`82
`2.80
`134.4
`178.2
`1000.0
`2.92
`143.0 109.6 -22.6 ahd
`B2
`69
`2.93
`148.3
`179.4
`-78..9
`9.92
`136.1 111.6
`13.8 =9a.8
`71
`80
`3,06
`1357.2
`176.8
`-126.0
`2.68
`131.0 109.7
`16.3-I08.2
`80
`FL
`2.98
`234.2
`179.4
`=74.6
`78
`76
`3.42 Te.
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`3.23
`94.0 134.9 38.0-b49,8
`83
`81
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`-140.7
`2.95
`128.1 130.3
`36..2-200.0
`@.
`114
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`1000.0
`2.92
`150.6 105.9
`7.9
`94.0
`114
`92
`2.94
`161.8
`=—175.1
`54.3
`3,27
`94.1 135.2 40.0-143.1
`34
`92
`169.5
`=134.6
`2.85
`141.6 109.1 -18.5 77.5
`94
`112
`=178.4
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`3.03
`126.5 128.5
`4.1
`70.6
`1n2
`94
`-178.8
`~144.1
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`97.7 127.5 40.6-Len?
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`93
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`-80.8
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`172.0 120.4
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`98
`107
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`101.1 123.8 64.0-154.9
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`179.8
`23.1
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`-84.2
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`178.1
`1000.0
`179.9
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`177.8
`-81.2
`177.9
`-64.6
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`125.6
`1.6
`122.2 6.4
`1ia.2 90.2
`131.7
`38.6
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`167, 8.
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`94.3
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`Page 23 of 90
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`Page 24 of 90
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`Page 24 of 90
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`Page 25 of 90
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`Project No.
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`Dihedral Angles for ARCHETYPE
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`153.6 125.5
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`164.
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`174.1
`112.
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`143.1 122.9 -0.6 50,
`176.6
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`164.4 125.2
`46.9 -42.
`179.7
`155.
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`9)
`«66,9 128.7
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`8)
`347.7 120.6
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`.95
`143.6 126.7
`-3.2 -63.
`177.6
`144.
`0 10.7 199.7
`«8315-7
`168.7
`“id.
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`.89
`156.1 102.0
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`.31
`143.8 133.7 -10.8 -5S.
`179.7
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`159.4 121.0 -15.8 -49,
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`149.
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`-83
`166.5 112.0 -15.6 ~88.
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`.87*
`150.9 117.6
`6.1
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`170.9 111.0
`12.6
`15.
`178.3
`138.
`M4
`153.7 123.9
`15.2
`48,
`177 4
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`(198.4 137.4
`-3.4 74,
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`TO00 111.7
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`175.
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`164.3 128.4
`8.6 -23.
`179.6
`i157.
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`148.3 114.1
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`134.3 122.2
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`164.1 117.8 -32.2 ag,
`178.5
`145.
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`«79.4 116.4 -75.1-131.
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`.81@ 127.9 108.6 -17.2-101,
`.00*
`160.6 109.9
`44.4 163,
`“L?.
`167.7
`.35
`«130.5 119.5
`14.3
`69.
`174.0
`145.
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`.46
`«72.8 125.3 ~64. 7-128,
`177.3
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`177.3
`139.
`.48@ 100.3 107.6 -10.9 -90.
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`166.9 1390.5
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`173.4
`44
`UBi.4 129.9 0,
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`62.9 198,0
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`49.
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`135.
`“112.
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`157.
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`174.7
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`177.4
`104.
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`117.
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`i72.
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`45.
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`Witnessed & Understood by me,
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`To Page No.
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`Page 26 of 90
`
`Page 26 of 90
`
`

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