1. OASIS-2004 A direct-method program for
Institute of Physics, CAS, Beijing, P.R. China
A direct-method program for
ab initio phasing and reciprocal-space
fragment extension with SAD/SIR data

2. People who contributed to the demonstration
Yuan-xin Gu, Cheng Yang,
Jia-wei Wang, Sheng Huang
De-qiang Yao & Hai-fu Fan

3. OASIS-2004 application Xylanase Contoured at 1s Space group: P21
Unit cell: a = 41.07, b = 67.14, c = 50.81Å
b = 113.5o
Resolution limit: 1.75Å; Multiplicity: 15.9
Anomalous scatterer: S (5 )
X-rays: synchrotron radiation
l = 1.488Å; D f ” = 0.52
Bijvoet ratio: <|DF |>/<F > = 0.56%
Phasing: OASIS 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

4. TT0570 OASIS-2004 application Space group: P21212 Unit cell:
Data courtesy of Professor Isao Tanaka & Dr. Nobuhisa Watanabe
Graduate School of Science, Hokkaido University, Japan
Space group: P21212
Unit cell:
a =
b =
c = Å
Number of residues
in the ASU: 1206
Resolution range: Å
Multiplicity: 20.9
Anomalous scatterer: S (22)
Wavelength:
l = 2.291Å; Df ” = 1.14
Bijvoet ratio: <|DF|>/<F> = 1.16%
Phasing:
OASIS DM (Cowtan)
Model building:
RESOLVE BUILD & ARP/wARP
ARP/wARP found 1153 of the total 1206 residues after 2 cycles of iteration
OASIS-2004
application

5. Better initial SAD phases

6. Phase information available in SAD
Bimodal distribution
of SAD
The phase of F”
Phase information available in SAD
Cochran
distribution
Peaked at
any where
from 0 to 2p
Peaked at
Sim
distribution

7. Two different kinds of initial SAD phases + PSim PBimodal
Sim-modified phases
PSim PCochran P+ P+ + P
P+-modified phases

8. Cover figure of Acta Cryst. D60, Part 11 (2004)
Se-SAD
Histone Methyltransferase Set 7/9
Space group: P212121
Unit cell: a = 66.09, b = 82.83, c = Å
Number of residues in ASU: 560
Number of independent reflections: 16352
Resolution limit: 2.8Å
Multiplicity: 3.8
Anomalous scatterer: Se(12)
l = Å; Df’ = -7.5, Df” = 6.5
Bijvoet ratio: <|DF|>/<F> = 7.03%
SAD phasing by OASIS DM
Data provided by Dr. S. J. Gamblin
and Dr. B. Xiao
Cover figure of Acta Cryst. D60, Part 11 (2004)

9. Comparison of the two types of initial phases
using 4 typical reflections from the protein
histone methyltransferase SET 7/9

10. Comparison on cumulative phase errors
sorted in descending order of Fobs
Number of reflections
Errors of Sim-modified phases ( o )
Errors of P+-modified phases ( o )
1500
57.1
45.8
3000
57.1
49.1
4500
56.5
50.0
6000
57.0
51.2
7500
57. 8
52.9
9000
58.7
54.1
10500
59.4
55.6
12000
60.8
56.9
13500
61.9
58.4
15000
63.4
60.2
16352
65.2
62.3

11. 2. Inclusion and auto balance of the
lack-of-closure error in the direct-method
phasing formula

12. Automatic solution of protein structures OASIS-2004 DM ARP/wARP
by a single run of +
Pepstatin-insenstive carboxylproteinase Br-SAD
Porcine Pancreatic Elastase
Xe-SAD
Lysozyme
S-SAD

13. OASIS-2004 application Pepstatin-insenstive carboxylproteinase
Contoured at 1s
Pepstatin-insenstive carboxylproteinase
Space group: P62
Unit cell: a = b = 97.31, c = 82.94Å, g = 120o
Resolution limit: 1.8Å; Multiplicity: 5.45
Anomalous scatterer: Br (13)
X-rays: synchrotron radiation
l = Å; D f ” = 5.0
Bijvoet ratio: <|D F |>/<F > = 7.06%
Phasing: OASIS DM (Cowtan)
Model building:
ARP/wARP found 358 of the total 372 residues
Data courtesy of Dr. Z. Dauter,
National Cancer Institute, USA

14. OASIS-2004 application Porcine Pancreatic Elastase Contoured at 1s
Space group: P212121
Unit cell: a = 50.2, b = 58.1, c = 74.3Å
Resolution limit: 1.94Å;
Total rotation range: 360o
Anomalous scatterer: Xe (1)
X-rays: synchrotron radiation
l = 2.1Å; D f ” = 11.8
Bijvoet ratio: <|D F |>/<F > = 5.76%
Phasing: OASIS DM (Cowtan)
Model building:
ARP/wARP found 236 of the total 240
residues
Data courtesy of Dr. M. S. Weiss, EMBL
Hamburg Outstation, c/o DESY, Germany

15. OASIS-2004 application Lysozyme Contoured at 1s Space group: P43212
Unit cell: a = 78.81, c = 36.80Å
Atoms in the asymmetric unit: 1001
Resolution limit: 1.53Å; Multiplicity: 23
Anomalous scatterer: S (10), Cl (7)
X-rays: synchrotron radiation
l = 1.54Å; D f ” = 0.56, 0.70
Bijvoet ratio: <|D F |>/<F > = 1.55%
Phasing: OASIS DM (Cowtan)
Model building:
ARP/wARP found 128 of the total 129
residues
Data courtesy of Dr. Z. Dauter,
National Cancer Institute, USA

16. 3. Dual-space fragment extension
Partial
model No
Yes
Reciprocal-space
fragment extension by
OASIS DM
Real-space
RESOLVE BUILD
and/or ARP/wARP
OK?
End

17. Azurin
Cu-SAD
Synchrotron l = 0.97Å
Cycle 3
95%
Azurin
Cu-SAD
Synchrotron l = 0.97Å
Cycle 0
42%
Xylanase S-SAD
Synchrotron
l = 1.49Å
99%
Cycle 6
25%
Cycle 0
Xylanase S-SAD
Synchrotron
l = 1.49Å
Lysozyme
S-SAD
Cr-Ka
98%
Cycle 6
52%
Cycle 0
Lysozyme
S-SAD
Cr-Ka
Glucose
isomerase
S-SAD
Cu-Ka
17%
Cycle 0
97%
Cycle 6
Glucose
isomerase
S-SAD
Cu-Ka
Cr-Ka
Se, S-SAD
Alanine racemase
Cycle 4
97%
Cr-Ka
Se, S-SAD
Alanine racemase
Cycle 0
52%

19. OASIS-2004 application Xylanase Contoured at 1s Space group: P21
Unit cell: a = 41.07, b = 67.14, c = 50.81Å
b = 113.5o
Resolution limit: 1.75Å; Multiplicity: 15.9
Anomalous scatterer: S (5 )
X-rays: synchrotron radiation
l = 1.488Å; D f ” = 0.52
Bijvoet ratio: <|DF |>/<F > = 0.56%
Phasing: OASIS 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

20. Improvement on electron-density map and automatic model building
Cycle 0
Cycle 3
Cycle 6
Improvement on electron-density map and
automatic model building

21. Thank you!