4ONZ
Crystal structure of a putative glycoside hydrolase (BACOVA_02161) from Bacteroides ovatus ATCC 8483 at 1.85 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4 | 293 | 1.0M lithium chloride, 20.0% polyethylene glycol 6000, 0.1M citric acid pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.09 | 41.25 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.575 | α = 90 |
b = 50.331 | β = 94.38 |
c = 85.631 | 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 | PIXEL | DECTRIS PILATUS 6M | Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) | 2013-11-26 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.91837,0.97953,0.97899 | SSRL | BL11-1 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.85 | 29.521 | 96.9 | 0.096 | 7.7 | 3.2 | 28087 | 28087 |
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 | 1.85 | 1.9 | 94.3 | 0.62 | 0.62 | 1.2 | 3.1 | 2038 |
Refinement
Statistics | |||||||||||||||||||
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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 | 1.85 | 29.521 | 28082 | 1433 | 96.53 | 0.1585 | 0.1562 | 0.2014 | RANDOM | 26.3568 |
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] | |
-0.57 | -0.56 | 0.49 | 0.13 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.8 |
r_dihedral_angle_4_deg | 11.18 |
r_dihedral_angle_3_deg | 9.739 |
r_dihedral_angle_1_deg | 3.627 |
r_mcangle_it | 2.561 |
r_mcbond_it | 1.606 |
r_mcbond_other | 1.606 |
r_angle_refined_deg | 1.413 |
r_angle_other_deg | 0.731 |
r_chiral_restr | 0.084 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2722 |
Nucleic Acid Atoms | |
Solvent Atoms | 268 |
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 |
REFMAC | refinement |
MOSFLM | data reduction |
SHELXD | phasing |