1. Solving Crystal Structures
A tiny team in the
Institute of Physics
dedicated to
Methods of
Solving Crystal Structures

2. Our target is
the phase problem in
X-ray Crystallography and
Electron microscopy
The application field of
our research outcome covers
Material Science and Life Science

3. Road Map

4. X-ray crystallography Electron microscopy
Acting as a tool of
image processing
Direct methods
Dealing with
pseudo symmetries
Pseudo
centro symmetry
Pseudo translational
symmetries
Two-stage
image processing
Enantiomorphous
phase ambiguity
Translational
phase ambiguity
Direct determination of
modulated structures from
electron diffraction data
Phasing protein
OAS and SIR data
Ab initio solution
of superstructures
Ab initio solution
of incommensurate and
composite structures

5. Freely available at http://cryst.iphy.ac.cn
Our products
SAPI (1985 – 1995)
DIMS (1994 – 1997)
VEC (1995 – 2000)
OASIS (2000 – )
(1985 – 1995)
(1994 – 1997)
(1995 – 2000)
(2000 – 20??)
Freely available at

6. The program VEC
More than 1000 copies of the program have been distributed in 66 countries/areas

7. Original EM from Prof. N. Uyeda
Symmetry
averaging
ED from Prof N. Uyeda
Original EM from Prof. N. Uyeda
Two-Step Image Processing
Image
Decon-
volution
Phase
extension
Fourier
recycling
Search for defocus
Partial
structure
model
Complete

8. Image Processing of Bi-2212 Deconvolution FT-1 Phase extension
Space group: N [Bbmb]
a = 5.42, b = 5.44, c = 30.5Å
q = 0.21b* + c*
EM image courtesy of Dr. S. Horiuchi
Deconvolution
FT-1 c b Bi Sr Cu Ca
Oxygen in Cu-O layer
Phase
extension

9. OASIS-2004 A direct-method program for
ab initio phasing and reciprocal-space
fragment extension with SAD/SIR data

10. Features:
Product of Cochran and Sim distributions rather than the Sim distribution alone is used for discrimination of experimental bimodal SAD distribution;
Auto scaled coefficient taking account of experimental lack-of-closure error is introduced to the direct-method phasing formula;
Reciprocal-space fragment extension is made possible by feeding back partial-structure information to the direct-method phasing. The combination of OASIS-2004, DM, RESOLVE (build only) and ARP/wARP can perform a dual-space fragment extension. This enables a fragment as small as ~20% to be automatically expanded to more than 95% of the complete structure.

11. 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

12. 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

13. OASIS-DM-(RESOLVE BUILD, ARP/wARP) Iteration
- Partial model from
RESOLVE BUILD
or ARP/wARP
Phase error in degrees 70 60 50 40 30 20 80 10
Cycle 5 1 6 2 4 3
OASIS-DM-(RESOLVE BUILD, ARP/wARP) Iteration
Xylanase sulfur-SAD phasing
Synchrotron radiation l = 1.49Å, <DF>/<F> = 0.56%
Is OASIS-2004
necessary?

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

15. 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

16. My colleagues (last 5 years):
Prof. Gu, Yuan-xin
Prof. Zheng, Chao-de
Mr. He, Yao
Mr. Yao, De-qiang
Dr. Hao, Quan
Dr. Chen, Jian-rong
Dr. Wang, Jia-wei
Dr. Huang, sheng

17. Thank you!