oasis-2006
DESCRIPTION
OASIS-2006. Institute of Physics Chinese Academy of Sciences Beijing 100080, P.R. China. http://cryst.iphy.ac.cn. OASIS ( 2000 ). in CCP4. OASIS - 2004. on the Web. OASIS - 2006. on the Web soon. OASIS-2006 GUI for CCP4i. Functions of OASIS. 1. Direct-method 2. Reciprocal-space. - PowerPoint PPT PresentationTRANSCRIPT
OASIS-2006OASIS-2006Institute of Physics
Chinese Academy of SciencesBeijing 100080, P.R. China
Institute of PhysicsChinese Academy of Sciences
Beijing 100080, P.R. China
http://cryst.iphy.ac.cnhttp://cryst.iphy.ac.cn
OASIS (2000)OASIS (2000) in CCP4in CCP4
OASIS-2004OASIS-2004 on the Webon the Web
OASIS-2006OASIS-2006 on the Websoon
on the Websoon
1. Direct-method
2. Reciprocal-space
1. Direct-method
2. Reciprocal-space
Functions of OASIS Functions of OASIS
SAD/SIR PhasingSAD/SIR Phasing
Fragment ExtensionFragment ExtensionFragment ExtensionFragment ExtensionDual-spaceDual-space
by combining with
DM, RESOLVE and ARP/wARPby combining with
DM, RESOLVE and ARP/wARP
Why direct methods?Why direct methods?
For better initial SAD phases!
For better initial SAD phases!
Bimodal distributionfrom SAD
" " "
The phase ofF”
P
Phase information available in SAD
Cochrandistribution
Peaked atany where
from 0 to 2
Peaked at
"2
Sim distribution
Two different kinds of initial SAD phases
P+-modified phases
P++P
PSim PBimodal Sim-modified phases
P+
PSim PCochran
" h h h1
" is the phase of " "exp 2N
j jj
i f i
h h h rF
1 1cos 2 " cos2 "
F h
h h h hh
F F FF
2 ' 'E E E h h h h 3 ' '" " " h h h h
1tan( ) 2 ( ) sin cos
2best P
h h h h
1
2 21 1exp 2 2 1 cos2 cos2
2 2m P
2h h h h h
,
2 2
2U T
pN N
j jj j
E E
Z Z
h h ' " h h h
, 3
1 1tanh sin
2 2
sin sin
c
best best
P
m m
h h
h' h h' h h' h' h h' hh'
Comparison of cumulative phase errors in descending order of Fobs
Comparison of cumulative phase errors in descending order of Fobs
60.263.415000
58.461.913500
56.960.812000
62.365.216352
55.659.410500
54.158.79000
52.957. 87500
51.257.06000
50.056.54500
49.157.13000
45.857.11500
Errors of PErrors of P++-modified -modified
phases phases (( oo ))Number of reflectionsNumber of reflections Errors of Sim-modified Errors of Sim-modified
phases phases (( oo ))
Histone methyltransferase SET 7/9
Reciprocal-space fragment extension
OASIS + DM
Reciprocal-space fragment extension
OASIS + DM
Dual-space fragment extensionDual-space fragment extension
, 3
1 1tanh sin
2 2
s s inin
best best
P
m m
h h
h' h h' h h' h' hh h'h'
, 3
1 1tanh sin
2 2
s s inin
best best
P
m m
h h
h' h h' h h' h' hh h'h'
Real-spacefragment extension
RESOLVE BUILD and/or ARP/wARP
Real-spacefragment extension
RESOLVE BUILD and/or ARP/wARP
Partialstructure
Partialstructure
NoNo
YesYes
OK?OK?
EndEnd
PartialmodelPartialmodel
SHARP-SOLOMON-ARP/wARPSHARP-SOLOMON-ARP/wARP
XylanaseSpace group: P21 Unit cell: a = 41.07, b = 67.14, c = 50.81Å = 113.5o Number of residues in the ASU: 303 Resolution limit: 1.75Å; Multiplicity: 15.9Anomalous scatterer: S (5 ) X-rays:synchrotron radiation= 1.488Å; f ” = 0.52Bijvoet ratio: <|F |>/<F > = 0.56% Data courtesy of Dr. Z. Dauter, National Cancer Institute, USA
OASIS-DM-RESOLVE BUILDcycle 025%
OASIS-DM-ARP/wARPcycle 699%SHARP-DM-RESOLVE BUILDBP3-DM-RESOLVE BUILD
2.1Å 3.5Å 4.0Å
SAD phasing at different resolutionsTT0570 Cu-Kdata, <|F|>/<F> ~ 0.55%
SAD phasing at different resolutionsTT0570 Cu-Kdata, <|F|>/<F> ~ 0.55%
SOLVE/RESOLVE
SOLVE/RESOLVE +OASIS-DM-(RESOLVE BUILD)
Dual-space fragment extension based on SOLVE/RESOLVE resultsDual-space fragment extension based on SOLVE/RESOLVE results1LIA (d14) 2.8Å SIR data
SOLVE/RESOLVE map
Sigma_A map based on a model manually builtfrom the SOLVE/RESOLVE map
OASIS-DM mapbased on
the same model
Dual-space fragment extension based on SOLVE/RESOLVE resultsDual-space fragment extension based on SOLVE/RESOLVE results2GW1 3.3Å SAD data
SOLVE/RESOLVE map Sigma_A map OASIS-DM map
Dual-space fragment extension based on SOLVE/RESOLVE resultsDual-space fragment extension based on SOLVE/RESOLVE results2GW1 3.3Å SAD data
Fragment extension based on
molecular replacement
Finalmodel
acidic phospholipase A2124 residues
MRmodel
60 residues48 residues
DM-ARP/wARP-OASIS iteration
Cycle 1 Cycle 2 Cycle 3
DM-ARP/wARP iteration
Cycle 9 Cycle 11 Cycle 13
DM-ARP/wARP iteration
Fragment ExtensionFragment ExtensionDual-spaceDual-space
without SAD/SIR informationwithout SAD/SIR information
, 3
1 1tanh sin
2 2
sin si n
best best
P
m m
h h
h' h h' h h' h' hh h'h'
, 3
1 1tanh sin
2 2
sin si n
best best
P
m m
h h
h' h h' h h' h' hh h'h'
Partialstructure
Partialstructure " h 5%
the phase of atoms
randomly selected from the current model
" h 5%
the phase of atoms
randomly selected from the current model
" h h h" h h h
" . . "model modeli e h h h h" . . "model modeli e h h h h
Density modification
by DM
Density modification
by DM
NoNo
MRmodel
MRmodel
Phase improvement
by OASIS
Phase improvement
by OASISYesYes
EndEnd
Model building by
RESOLVE BUILD or ARP/wARP
Model building by
RESOLVE BUILD or ARP/wARP
OK?OK?
Sample: 1UJZSample: 1UJZSpace group: I 222Unit cell: a=62.88, b=74.55, c=120.44ÅNumber of residues in ASU: 215 molecule A: 87 residues molecule B: 128 residuesResolution range: 37.57 – 2.10ÅNumber of reflections: 16460
Space group: I 222Unit cell: a=62.88, b=74.55, c=120.44ÅNumber of residues in ASU: 215 molecule A: 87 residues molecule B: 128 residuesResolution range: 37.57 – 2.10ÅNumber of reflections: 16460
Range of phase error in degrees
Cycle 1 Cycle 3 Cycle 5 Cycle 7
Nr. of Reflns.
% of P+ > ½
Nr. of Reflns.
% of P+ > ½
Nr. of Reflns.
% of P+ > ½
Nr. of Reflns.
% of P+ > ½
0 - 30 4084 63 4571 69 4877 71 7226 82
30 - 60 3117 55 3262 57 3204 55 2490 47
60 - 90 2476 44 2330 41 2141 38 1622 21
90 - 120 2025 34 1873 30 1846 27 1466 12
120 -150 1881 31 1711 25 1667 22 1332 7
150 - 180 1766 25 1610 23 1610 17 1215 7
1UJZ Phase Statistics1UJZ Phase Statistics
DM-ARP/wARP-OASISiterationDM-ARP/wARP-OASISiteration
Cycle 1 Cycle 2 Cycle 3 Cycle 5 Cycle 7
1UJZ
FinalmodelFinalmodel215 residues
MRmodelMRmodel
54 residuesDM-ARP/wARP
iterationDM-ARP/wARP
iteration
Cycle 4
Hai-fu Fan1, Yuan-xin Gu1, Tao Jiang2, Zheng-jiong Lin2 & Chao-de Zheng1
Hai-fu Fan1, Yuan-xin Gu1, Tao Jiang2, Zheng-jiong Lin2 & Chao-de Zheng1
Participants of this projectParticipants of this projectStaffsStaffs
Ph.D. studentsPh.D. studentsJian-rong Chen1, Qiang Chen3, Yao He1,
Sheng Huang1,4, He Li2, Jia-wei Wang1, Li-jie Wu1, De-qiang Yao1,5 & Tao Zhang1,6
Jian-rong Chen1, Qiang Chen3, Yao He1, Sheng Huang1,4, He Li2, Jia-wei Wang1, Li-jie Wu1,
De-qiang Yao1,5 & Tao Zhang1,6
1 Institute of Physics, CAS, Beijing, China2 Institute of Biophysics, CAS, Beijing, China3 Peking University, Beijing, China4 Institute of High Energy Physics, CAS, Beijing, China5 Univ. of Science & Technology of China, Hefei, China6 Lanzhou University, Lanzhou, China
1 Institute of Physics, CAS, Beijing, China2 Institute of Biophysics, CAS, Beijing, China3 Peking University, Beijing, China4 Institute of High Energy Physics, CAS, Beijing, China5 Univ. of Science & Technology of China, Hefei, China6 Lanzhou University, Lanzhou, China
SAD data used in this presentationwere kindly provided by
SAD data used in this presentationwere kindly provided by
AcknowledgementsAcknowledgements
Dr. Z. Dauter1, Dr. S. J. Gamblin2, Dr. B. D. Sha3, Prof. I. Tanaka4, Dr. N. Watanabe4 & Dr. B. Xiao2
Dr. Z. Dauter1, Dr. S. J. Gamblin2, Dr. B. D. Sha3, Prof. I. Tanaka4, Dr. N. Watanabe4 & Dr. B. Xiao2
1 Argonne National Laboratory, USA2 The National Institute for Medical Research, UK3 Department of Cell Biology, University of Alabama at Birmingham, USA4 Graduate School of Science, Hokkaido University, Japan
1 Argonne National Laboratory, USA2 The National Institute for Medical Research, UK3 Department of Cell Biology, University of Alabama at Birmingham, USA4 Graduate School of Science, Hokkaido University, Japan