3PAJ
2.00 Angstrom resolution crystal structure of a quinolinate phosphoribosyltransferase from Vibrio cholerae O1 biovar eltor str. N16961
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1QAP | PDB ENTRY 1QAP |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 287 | Protein: 7 mg/mL in 10 mM Tris/HCl pH 8.3, 0.5 M NaCl, 5 mM BME. Crystallization condition: 0.2 M MgCl2, 0.1 M Bis-Tris, 25 % (w/v) PEG3350. Mixed 1:1 v/v., VAPOR DIFFUSION, SITTING DROP, temperature 287K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.99 | 38.27 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 59.195 | α = 90 |
b = 79.551 | β = 90 |
c = 117.908 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 2010-10-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | 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 | 30 | 99.8 | 0.081 | 22.98 | 7.1 | 38142 | 38142 | -3 | 21.6 |
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 | 2.03 | 100 | 0.279 | 9.76 | 7.3 | 1893 |
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 1QAP | 2 | 29.6 | 36159 | 36159 | 1908 | 99.68 | 0.17557 | 0.17312 | 0.22175 | RANDOM | 26.541 |
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] | |
0.69 | -0.92 | 0.22 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.254 |
r_dihedral_angle_4_deg | 10.904 |
r_dihedral_angle_3_deg | 9.32 |
r_scangle_it | 4.062 |
r_scbond_it | 2.406 |
r_dihedral_angle_1_deg | 2.058 |
r_angle_refined_deg | 1.609 |
r_mcangle_it | 1.323 |
r_angle_other_deg | 0.973 |
r_mcbond_it | 0.69 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4542 |
Nucleic Acid Atoms | |
Solvent Atoms | 414 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |