3CWX
Crystal structure of cagd from helicobacter pylori pathogenicity island
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 7 | 298 | 0.2 M MgGl2, 0.1M Hepes, 20% PEG 6000, pH 7, VAPOR DIFFUSION, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.26 | 45.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.181 | α = 90 |
b = 117.956 | β = 110.26 |
c = 65.157 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | 2006-12-07 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | 0.97942, 0.97420, 0.97814 | ESRF | ID14-4 |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.2 | 62.26 | 99.2 | 0.088 | 16.6 | 7.3 | 28577 | 28577 |
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) | |||||||||||
2.2 | 2.32 | 99.9 | 0.411 | 4.1 | 7.4 | 4107 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MAD | FREE R | 2.3 | 62.26 | 27833 | 27833 | 2783 | 99.6 | 0.242 | 0.242 | 0.288 | RANDOM |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
3361 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_similar_adp_cmpnt | 0.097 |
s_anti_bump_dis_restr | 0.032 |
s_non_zero_chiral_vol | 0.029 |
s_zero_chiral_vol | 0.024 |
s_from_restr_planes | 0.0232 |
s_angle_d | 0.019 |
s_bond_d | 0.005 |
s_similar_dist | |
s_rigid_bond_adp_cmpnt | |
s_approx_iso_adps |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3105 |
Nucleic Acid Atoms | |
Solvent Atoms | 158 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
SHARP | phasing |
SHELXL-97 | refinement |
MOSFLM | data reduction |
SCALA | data scaling |