4CV7
Crystal structure of Rhodococcus equi VapB
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | SITTING DROP VAPOUR DIFFUSION AT 293 K WITH 1 UL PROTEIN (10 MG/ML) PLUS 0.5 UL RESERVOIR SOLUTION CONSISTING OF 0.01 M COCL2, 0.1 M NA-ACETATE, PH 4.6, AND 1.0 M HEXANEDIOL (JCSG CORE II CONDITION G4). |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.79 | 56 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 83.82 | α = 90 |
b = 83.82 | β = 90 |
c = 49.13 | γ = 120 |
Symmetry | |
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Space Group | P 61 2 2 |
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 | 2012-11-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | ESRF | ID29 |
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 | 1.4 | 50 | 100 | 0.1 | 26.9 | 37 | 20584 | -3 |
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 | 1.4 | 1.44 | 100 | 1.26 | 2.67 | 29 |
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 | SAD | THROUGHOUT | 1.4 | 50 | 18526 | 2030 | 99.95 | 0.17252 | 0.16972 | 0.19854 | RANDOM | 20.913 |
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] | |
0.29 | 0.14 | 0.29 | -0.92 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_angle_refined_deg | 2.234 |
r_mcangle_it | 1.675 |
r_scbond_it | 1.618 |
r_mcbond_it | 1.141 |
r_mcbond_other | 1.139 |
r_angle_other_deg | 1.039 |
r_chiral_restr | 0.155 |
r_bond_refined_d | 0.024 |
r_gen_planes_refined | 0.015 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 840 |
Nucleic Acid Atoms | |
Solvent Atoms | 107 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
SHELXD | phasing |