3DZM
Crystal structure of a major outer membrane protein from Thermus thermophilus HB27
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 9 | 291 | 0.2M sodium malonate, 44% MPD, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
2 | VAPOR DIFFUSION, HANGING DROP | 9 | 291 | 0.2M sodium malonate, 43% MPD, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 166.98 | α = 90 |
b = 166.98 | β = 90 |
c = 98.12 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | mirrors | 2008-03-01 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 100 | PIXEL | PSI PILATUS 6M | mirrors | 2008-04-09 | M | SINGLE WAVELENGTH | |||||
3 | 1 | x-ray | 100 | PIXEL | PSI PILATUS 6M | mirrors | 2008-05-05 | M | SINGLE WAVELENGTH | |||||
1,2,3 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 1.072 | ESRF | ID23-1 |
2 | SYNCHROTRON | SLS BEAMLINE X06SA | 0.9252 | SLS | X06SA |
3 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.0162 | SLS | X06SA |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1,2,3 | 2.8 | 40 | 99.5 | 0.097 | 9.8 | 38811 | 38811 | -3 | 86.43 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1,2,3 | 2.8 | 2.97 | 97.2 | 1.034 | 1.42 | 10.1 | 6196 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | SIRAS | 2.801 | 37.126 | 2 | 38810 | 38810 | 1946 | 99.53 | 0.198 | 0.196 | 0.234 | 5% of reflections, selected randomly | 100.676 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.925 | 0.925 | -1.85 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 20.892 |
f_angle_d | 1.649 |
f_chiral_restr | 0.102 |
f_bond_d | 0.013 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 4626 |
Nucleic Acid Atoms | |
Solvent Atoms | 41 |
Heterogen Atoms | 129 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |
SHARP | phasing |