4QOA
Crystal structure of a putative periplasmic protein (BACUNI_04550) from Bacteroides uniformis ATCC 8492 at 2.75 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 24.00% polyethylene glycol 3350, 0.16M tri-ammonium citrate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.77 | 74.21 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 103.311 | α = 90 |
b = 103.311 | β = 90 |
c = 90.83 | γ = 120 |
Symmetry | |
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Space Group | P 65 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator | 2014-03-27 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL12-2 | 0.9116,0.9794,0.9793 | SSRL | BL12-2 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.75 | 29.823 | 99.8 | 0.084 | 15.7 | 9.1 | 7860 | 7860 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.75 | 2.82 | 100 | 0.012 | 1.185 | 0.7 | 8.8 | 565 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | MAD | THROUGHOUT | 2.75 | 29.823 | 7840 | 361 | 99.83 | 0.2166 | 0.215 | 0.2498 | RANDOM | 87.8228 |
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] | |
14.8621 | 14.8621 | -29.7241 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_omega_torsion | 2.49 |
t_other_torsion | 2.27 |
t_angle_deg | 1.17 |
t_bond_d | 0.009 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_nbd | |
t_improper_torsion |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1005 |
Nucleic Acid Atoms | |
Solvent Atoms | 17 |
Heterogen Atoms | 8 |
Software
Software | |
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Software Name | Purpose |
MolProbity | model building |
PDB_EXTRACT | data extraction |
SHELX | phasing |
SHARP | phasing |
SCALA | data scaling |
BUSTER-TNT | refinement |
MOSFLM | data reduction |
SHELXD | phasing |
BUSTER | refinement |