SAD phasing by OASIS-2004 SAD phasing by OASIS-2004.
-
Upload
abner-francis -
Category
Documents
-
view
227 -
download
0
Transcript of SAD phasing by OASIS-2004 SAD phasing by OASIS-2004.
SAD phasingby OASIS-2004
SAD phasingby OASIS-2004
OASIS-2004OASIS-2004
Freely available at http://cryst.iphy.ac.cn
A program for direct-method phasing and reciprocal-space fragment extension with
SAD/SIR data
By J.W. Wang, Y.X. Gu*, C.D. Zheng, H.F. Fan*and Q. Hao
* Corresponding authors
SAD data used in this presentationwere kindly provided by
Dr. Z. Dauter, Dr. S. J. Gamblin, Prof. S. Hasnain, Prof. I. Tanaka, Dr. N. Watanabe, Dr. M.S. Weiss, D
r. B. Xiao and Dr. C. Yang
Calculations were done by
Mr. D.Q. Yao, Dr. S. Huang and Dr. J.W. Wang
Acknowledgements
Two examples ondifficult SAD phasing
Two examples ondifficult SAD phasing
OASIS-2004application
Contoured at 1
XylanaseSpace group: P21 Unit cell: a = 41.07, b = 67.14, c = 50.81Å = 113.5o Resolution limit: 1.75Å; Multiplicity: 15.9Anomalous scatterer: S (5 ) X-rays:synchrotron radiation= 1.488Å; f ” = 0.52Bijvoet ratio: <|F |>/<F > = 0.56% Phasing: OASIS-2004 + DM (Cowtan)Model building: RESOLVE BUILD & ARP/wARP found 299 of the total 303 residues at the 6th cycle of iteration Data courtesy of Dr. Z. Dauter, National Cancer Institute, USA
TT0570
Data courtesy of Professor Isao Tanaka & Dr. Nobuhisa WatanabeGraduate School of Science, Hokkaido University, Japan
Space group: P21212 Unit cell: a = 100.2639 b = 108.9852 c = 114.6272ÅNumber of residues in the ASU: 1206Resolution range: 50.00-2.01ÅMultiplicity: 20.9Anomalous scatterer: S (22) Wavelength: = 2.291Å; f ” = 1.14Bijvoet ratio: <|F|>/<F> = 1.16%Phasing: OASIS-2004 + DM (Cowtan)Model building: RESOLVE BUILD & ARP/wARP
ARP/wARP found 1153 of the total 1206 residues after 2 cycles of iteration
OASIS-2004application
Features ofFeatures of
OASIS-2004OASIS-2004
1. Better initial SAD phases1. Better initial SAD phases
" h h h" h h h
1tan( ) 2 ( ) sin cos
2best P
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
12 21 1
exp 2 2 1 cos2 cos22 2
m P
2h h h h h
, 3
1 1tanh sin
2 2
sin sinbest bes
c
t
P
m m
h h
h' h h' h h' h' h h' hh'
, 3
1 1tanh sin
2 2
sin sinbest bes
c
t
P
m m
h h
h' h h' h h' h' h h' hh'
Bimodal distributionof SAD
" " "
The phase ofF”
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++P
PSim PBimodal Sim-modified phases
P+-modified phases
P+
PSim PCochran
Se-SAD
Histone Methyltransferase Set 7/9Space group: P212121
Unit cell: a = 66.09, b = 82.83, c = 116.15ÅNumber of residues in ASU: 560
Number of independent reflections: 16352Resolution limit: 2.8Å
Multiplicity: 3.8Anomalous scatterer: Se(12)
= 0.9794Å; f’ = -7.5, f” = 6.5 Bijvoet ratio: <|F|>/<F> = 7.03%
SAD phasing by OASIS-2004 + DMData provided by Dr. S. J. Gamblin
and Dr. B. Xiao
Comparison of the two kinds of initial phasesusing 4 typical reflections from the protein
histone methyltransferase SET 7/9
Comparison on cumulative phase errors sorted in descending order of Fobs
Comparison on cumulative phase errors sorted 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 ))
2
22
2 "
Fn
F
h
h
h
2
22
2 "
Fn
F
h
h
h
2. Inclusion and auto balance of the lack-of-closure error in the direct-method phasing formula
2. Inclusion and auto balance of the lack-of-closure error in the direct-method phasing formula
1 2
21 1
exp 2 2 1 cos2 cos22 2
m P
2h h h h
1 22
1 1exp 2 2 1 cos2 cos2
2 2m P
2h h h h
, 3
1 1
2 2
tanh sin sin sinbest best
P
m m
h
h h' h h' h h' h' h h' hh'
, 3
1 1
2 2
tanh sin sin sinbest best
P
m m
h
h h' h h' h h' h' h h' hh'
1exp 2
2 2h 1
exp 22
2h
Automatic solution of protein structures
OASIS-2004 DM
Automatic solution of protein structures
OASIS-2004 DM
by a single run ofby a single run of
RESOLVE(Build only)
and/or
ARP/wARP
RESOLVE(Build only)
and/or
ARP/wARP
++ ++
Br-SADOASIS-2004application
Contoured at 1
Pepstatin-insenstive carboxylproteinaseSpace group: P62
Unit cell: a = b = 97.31, c = 82.94Å, = 120o
Resolution limit: 1.8Å; Multiplicity: 5.45Anomalous scatterer: Br (13)X-rays:synchrotron radiation= 0.9191Å; f ” = 5.0 Bijvoet ratio: <| F |>/<F > = 7.06% Phasing: OASIS-2004 + DM (Cowtan)Model building: ARP/wARP found 358 of the total 372 residuesData courtesy of Dr. Z. Dauter, National Cancer Institute, USA
Xe-SADOASIS-2004application
Contoured at 1
Porcine Pancreatic Elastase Space group: P212121 Unit cell: a = 50.2, b = 58.1, c = 74.3ÅResolution limit: 1.94Å; Total rotation range: 360o
Anomalous scatterer: Xe (1)X-rays:synchrotron radiation= 2.1Å; f ” = 11.8 Bijvoet ratio: <| F |>/<F > = 5.76% Phasing: OASIS-2004 + DM (Cowtan)Model building: ARP/wARP found 236 of the total 240 residuesData courtesy of Dr. M. S. Weiss, EMBL Hamburg Outstation, c/o DESY, Germany
S-SADOASIS-2004application
Contoured at 1
Lysozyme Space group: P43212
Unit cell: a = 78.81, c = 36.80ÅAtoms in the asymmetric unit: 1001Resolution limit: 1.53Å; Multiplicity: 23Anomalous scatterer: S (10), Cl (7)X-rays:synchrotron radiation= 1.54Å; f ” = 0.56, 0.70 Bijvoet ratio: <| F |>/<F > = 1.55% Phasing: OASIS-2004 + DM (Cowtan)Model building: ARP/wARP found 128 of the total 129 residuesData courtesy of Dr. Z. Dauter, National Cancer Institute, USA
Cu-K
Fe-SAD
302 residues found automatically
YfbpASpace group: P212121 Unit cell: a = 42.792, b = 54.134, c = 115.222ÅResolution range: 57.74 – 1.42ÅAnomalous scatterer: Fe (1)Wavelength: 1.542Åf ” = 3.20<|F|>/<F> ~ 1.4%Phased by: OASIS + DM (Cowtan)Automatic model building by: ARP/wARPData provided by Dr. Cheng Yang Rigaku/MSC, USA
OASIS-2004 application
3. Dual-space fragment extension3. Dual-space fragment extension
, 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'
PartialmodelPartialmodel
PartialmodelPartialmodel
NoNoYesYes
Reciprocal-spacefragment extension by
OASIS-2004 + DM
Reciprocal-spacefragment extension by
OASIS-2004 + DM
Real-space fragment extension by
RESOLVE BUILD and/or ARP/wARP
Real-space fragment extension by
RESOLVE BUILD and/or ARP/wARP
OK?OK?
End End
Glucoseisomerase
S-SADCu-K
17%Cycle 097%Cycle 6
Glucoseisomerase
S-SADCu-K
Cr-K Se, S-SAD Alanine racemase
Cycle 052%
Cr-K Se, S-SAD Alanine racemase
Cycle 497%
25%Cycle 0
Xylanase S-SADSynchrotron = 1.49Å
Xylanase S-SADSynchrotron = 1.49Å
99%Cycle 6
52%Cycle 0
LysozymeS-SADCr-K
LysozymeS-SADCr-K
98%Cycle 6 Azurin
Cu-SADSynchrotron = 0.97Å
Cycle 042%
AzurinCu-SADSynchrotron = 0.97Å
Cycle 395%
Case studyCase study1. Azurin
2. Xylanase1. Azurin
2. Xylanase
Contoured at 1
Space group: P4122 Unit cell: a = b = 52.65, c = 100.63ÅResolution limit: 1.9Å; Multiplicity: 10.0 Anomalous scatterer: Cu (1)X-rays: Synchrotron radiation =0.97Å;f” = 2.206; <|F|>/<F> = 1.44%Phasing: OASIS-2004 + DM (Cowtan)Model building: RESOLVE BUILD and ARP/wARP116 of 129 residues found automaticallyData courtesy of Professor S. Hasnain
Azurin
70
60
50
40
30
80
OASIS-2004
DM
Partial model from RESOLVE BUILD or ARP/wARP
Cycle0 1 2 43
Ph
ase
erro
r in
deg
rees
OASIS-DM-(RESOLVE BUILD, ARP/wARP) IterationAzurin copper-SAD phasing
Synchrotron radiation = 0.97Å, <F>/<F> = 1.44%P
has
e er
ror
in d
egre
es
What would it bewithout using
RESOLVE (build only)?
Is OASISnecessaryhere? Is OASIS
necessaryhere?
OASIS-DM-ARP/wARP IterationAzurin copper-SAD phasing
Synchrotron radiation = 0.97Å, <F>/<F> = 1.44%
OASIS-DM-ARP/wARP IterationAzurin copper-SAD phasing
Synchrotron radiation = 0.97Å, <F>/<F> = 1.44%P
has
e er
ror
in d
egre
es
0 102 4 86
Cycle
70
60
50
40
30
80
70
60
50
40
30
80
OASIS-2004
DM
Partial model from ARP/wARP
Cycle 0(ARP/wARP)
Cycle 4(ARP/wARP)
Cycle 6(ARP/wARP)
Cycle 8(ARP/wARP)
OASIS-DM-ARP/wARP Iteration
Cycle 0(RESOLVE BUILD)
Cycle 1(ARP/wARP)
Cycle 2(ARP/wARP)
Cycle 3(ARP/wARP)
OASIS-DM-(RESOLVE BUILD, ARP/wARP) Iteration
Cycle 10(ARP/wARP)
Cycle 4(ARP/wARP)
Cycle 0Cycle 0 Cycle 2Cycle 2 Cycle 4Cycle 4
Improvement on electron-density map andautomatic model building
Improvement on electron-density map andautomatic model building
Cycle 0Cycle 0 Cycle 2Cycle 2 Cycle 4Cycle 4
Xylanase
Contoured at 1
Space group: P21 Unit cell: a = 41.07, b = 67.14, c = 50.81Å = 113.5o Resolution limit: 1.75Å; Multiplicity: 15.9Anomalous scatterer: S (5 ) X-rays:synchrotron radiation= 1.488Å; f ” = 0.52Bijvoet ratio: <|F |>/<F > = 0.56% Phasing: OASIS-2004 + DM (Cowtan)Model building: RESOLVE BUILD & ARP/wARP found 299 of the total 303 residues at the 6th cycle of iteration Data courtesy of Dr. Z. Dauter, National Cancer Institute, USA
OASIS-2004
DM
Partial model from RESOLVE BUILD or ARP/wARP
Ph
ase
erro
r in
deg
rees
70
60
50
40
30
20
80
10
Cycle0 51 62 43
OASIS-DM-(RESOLVE BUILD, ARP/wARP) IterationXylanase sulfur-SAD phasing
Synchrotron radiation = 1.49Å, <F>/<F> = 0.56%Is OASISnecessaryhere?
What would it bewithout using
RESOLVE (build only)?
Is OASISnecessaryhere?
OASIS-DM-ARP/wARP IterationXylanase sulfur-SAD phasing
Synchrotron radiation = 1.49Å, <F>/<F> = 0.56%
OASIS-DM-ARP/wARP IterationXylanase sulfur-SAD phasing
Synchrotron radiation = 1.49Å, <F>/<F> = 0.56%
70
60
50
40
30
20
80
0 102 124 86 14 16
Ph
ase
erro
r in
deg
rees
Cycle
OASIS-2004
DM
Partial model from ARP/wARP
Cycle 14(ARP/wARP)
Cycle 16(ARP/wARP)
Cycle 17(ARP/wARP)
Cycle 0(ARP/wARP)
Cycle 0(RESOLVE BUILD)
Cycle 3(ARP/wARP)
Cycle 5(ARP/wARP)
Cycle 6(ARP/wARP)
OASIS-DM-ARP/wARP Iteration
OASIS-DM-(RESOLVE BUILD, ARP/wARP) Iteration
Cycle 0Cycle 0 Cycle 3Cycle 3 Cycle 6Cycle 6
Improvement on electron-density map andautomatic model building
Improvement on electron-density map andautomatic model building
ConclusionConclusion
1. OASIS is essential for initial SAD phasing and for initiating a successful dual-space fragment
extension;
2. Starting models from RESOLVE (build only) lead much faster to the final solution;
3. ARP/wARP models with dummy atoms only may lead to nearly the complete structure after
sufficient cycles of iteration.
Thank you!Thank you!