4OHC
Crystal structure of orotate phosphoribosyltransferase (OPRTase) from Burkholderia cenocepacia
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 289 | JCSG+ g6: 200mM sodium malonate, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.54 | 51.57 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 76.31 | α = 105.83 |
b = 82.97 | β = 104.27 |
c = 83.1 | γ = 117.36 |
Symmetry | |
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Space Group | P 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 | RAYONIX MX225HE | 2013-12-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97872 | APS | 21-ID-G |
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 | 97.4 | 0.06 | 17.9 | 3.9 | 134209 | 130679 | 17.7 |
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 | 1.85 | 1.9 | 95.8 | 0.502 | 2.75 | 3.6 | 9459 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 3m3h | 1.85 | 50 | 124114 | 6564 | 97.62 | 0.15758 | 0.15556 | 0.19659 | RANDOM | 25.629 |
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] | |
0.06 | 0.24 | 0.51 | -0.57 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.289 |
r_dihedral_angle_4_deg | 18.029 |
r_dihedral_angle_3_deg | 12.985 |
r_long_range_B_refined | 7.787 |
r_long_range_B_other | 7.786 |
r_dihedral_angle_1_deg | 6.039 |
r_mcangle_it | 1.665 |
r_mcangle_other | 1.665 |
r_angle_refined_deg | 1.573 |
r_scangle_other | 1.462 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10303 |
Nucleic Acid Atoms | |
Solvent Atoms | 1175 |
Heterogen Atoms | 56 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |