4O5J
Crystal structure of SabA from Helicobacter pylori
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 293.15 | 200mM sodium acetate, 18-20% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
6 | 79.49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 180.044 | α = 90 |
b = 180.044 | β = 90 |
c = 64.47 | γ = 120 |
Symmetry | |
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Space Group | P 31 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 315r | 2013-03-14 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315r | 2013-02-13 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.9537 | Australian Synchrotron | MX2 |
2 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.9690, 0.9795 | Australian Synchrotron | MX2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.2 | 90.03 | 100 | 9.3 | 60972 | 60966 | 1 | 1 | 36.6 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1,2 | 2.2 | 2.32 | 100 | 1.03 | 0.357 | 2.4 | 9.3 | 8825 |
Refinement
Statistics | |||||||||||||||||||
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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 | THROUGHOUT | 2.2 | 90.02 | 60970 | 57908 | 3062 | 99.95 | 0.141 | 0.1409 | 0.1399 | 0.15939 | RANDOM | 57.126 |
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] | |
-0.08 | -0.04 | -0.08 | 0.13 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 63.685 |
r_sphericity_bonded | 52.249 |
r_dihedral_angle_2_deg | 40.752 |
r_dihedral_angle_4_deg | 20.571 |
r_dihedral_angle_3_deg | 14.509 |
r_rigid_bond_restr | 13.979 |
r_dihedral_angle_1_deg | 4.142 |
r_angle_refined_deg | 1.533 |
r_chiral_restr | 0.09 |
r_bond_refined_d | 0.02 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2839 |
Nucleic Acid Atoms | |
Solvent Atoms | 158 |
Heterogen Atoms | 14 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
Auto-Rickshaw | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |