3N2L
2.1 Angstrom resolution crystal structure of an Orotate Phosphoribosyltransferase (pyrE) from Vibrio cholerae O1 biovar eltor str. N16961
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.5 | 295 | 7.5 mg/mL protein in 10 mM Tris/HCl pH 8.3 0.5 M NaCl, 5 mM BME. The crystallization condition is The Classics II Suite (#8) Cryo 5M NaCl + 50% sucrose. Crystals grew from 1:1 v/v drop. , VAPOR DIFFUSION, SITTING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.36 | 47.78 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 96.587 | α = 90 |
b = 76.712 | β = 92.63 |
c = 133.944 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | MARMOSAIC 225 mm CCD | Be Lenses/Diamond Laue Mono | 2010-04-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97857 | APS | 21-ID-F |
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 | 2.1 | 30 | 99.7 | 0.079 | 11.25 | 3.9 | 114128 | 114128 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
2.1 | 2.14 | 99.6 | 0.495 | 2.72 | 3.7 | 5630 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | PDB entry 1LH0 | 2.1 | 30 | 108289 | 108289 | 5711 | 99.51 | 0.22436 | 0.222 | 0.26861 | RANDOM | 44.833 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.94 | 0.7 | -2.37 | 3.38 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 26.681 |
r_dihedral_angle_4_deg | 14.486 |
r_dihedral_angle_3_deg | 14.357 |
r_dihedral_angle_1_deg | 3.748 |
r_scangle_it | 3.576 |
r_scbond_it | 2.265 |
r_angle_refined_deg | 1.567 |
r_mcangle_it | 1.504 |
r_angle_other_deg | 0.867 |
r_mcbond_it | 0.837 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11639 |
Nucleic Acid Atoms | |
Solvent Atoms | 639 |
Heterogen Atoms | 3 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |