3F42
Crystal structure of uncharacterized protein HP0035 from Helicobacter pylori
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 297 | 30% PEG 4K,0.2M Ammonium Acetate, 0.1M Sodium Citrate pH5.6, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.19 | 43.72 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 87.129 | α = 90 |
b = 99.566 | β = 90 |
c = 45.196 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 | 2008-08-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | APS | 19-ID |
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 | 1.78 | 50 | 99.6 | 0.074 | 50.3 | 7.1 | 19258 | 19185 | -3 | 29.06 |
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 | 1.78 | 1.81 | 100 | 0.68 | 6.1 | 940 |
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 | SAD | THROUGHOUT | 1.78 | 50 | 19143 | 19143 | 982 | 99.44 | 0.1819 | 0.1819 | 0.17989 | 0.2198 | RANDOM | 28.204 |
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] | |
0.01 | -0.41 | 0.4 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.573 |
r_dihedral_angle_4_deg | 14.438 |
r_dihedral_angle_3_deg | 13.194 |
r_dihedral_angle_1_deg | 4.523 |
r_scangle_it | 4.409 |
r_scbond_it | 2.779 |
r_mcangle_it | 1.585 |
r_angle_refined_deg | 1.373 |
r_mcbond_it | 0.879 |
r_chiral_restr | 0.096 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1330 |
Nucleic Acid Atoms | |
Solvent Atoms | 142 |
Heterogen Atoms | 16 |
Software
Software | |
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Software Name | Purpose |
SBC-Collect | data collection |
HKL-3000 | phasing |
MLPHARE | phasing |
DM | model building |
SHELXD | phasing |
RESOLVE | model building |
Coot | model building |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
DM | phasing |
RESOLVE | phasing |