oasis-2004 institute of physics, cas, beijing, p.r. china a direct-method program for ab initio...

OASIS-2004OASIS-2004

Institute of Physics, CAS, Beijing, P.R. China

http://cryst.iphy.ac.cn

A direct-method program for ab initio phasing and reciprocal-space fragment extension with SAD/SIR data

People who contributedto the demonstration

People who contributedto the demonstration

Yuan-xin Gu, Cheng Yang, Jia-wei Wang, Sheng Huang De-qiang Yao & Hai-fu Fan

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

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

Cover figure of Acta Cryst. D60, Part 11 (2004)

Comparison of the two types 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 ARP/wARP

Automatic solution of protein structures

OASIS-2004 DM ARP/wARP by a single run ofby a single run of

++ ++Pepstatin-insenstive carboxylproteinase

Br-SAD

Pepstatin-insenstive carboxylproteinase

Br-SAD

Porcine Pancreatic ElastaseXe-SAD

Porcine Pancreatic ElastaseXe-SAD

Lysozyme

S-SAD

Lysozyme

S-SAD

OASIS-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

OASIS-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

OASIS-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

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%

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

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

Thank you!Thank you!