4H31
Crystal structure of anabolic ornithine carbamoyltransferase from Vibrio vulnificus in complex with carbamoyl phosphate and L-norvaline
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3UPD |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 5.5 | 289 | Protein: 10 mg/ml in 10 mM Tris-HCl pH 8.3, 20 mM Carbamoyl phosphate, 20 mM L-norvaline, 500 mM NaCl and 5 mM b-mercaptoethanol. Crystallization condition: 0.2 M Ammonium Acetate, 0.1 M Bis-Tris pH 5.5, 23% PEG 3350, VAPOR DIFFUSION, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.93 | 36.24 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 74.262 | α = 90 |
b = 80.911 | β = 90 |
c = 152.733 | 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 300 mm CCD | Be-Lenses | 2012-06-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.7 | 50 | 100 | 0.082 | 0.082 | 29.8 | 6.5 | 102701 | 102659 | -3 | 21.9 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.7 | 1.73 | 100 | 0.963 | 0.963 | 1.9 | 5.5 | 5067 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3UPD | 1.7 | 50 | 96750 | 96702 | 5088 | 99.95 | 0.13704 | 0.13704 | 0.13541 | 0.16735 | RANDOM | 25.753 |
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] | |
-1 | -0.04 | 1.04 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.631 |
r_dihedral_angle_4_deg | 14.34 |
r_dihedral_angle_3_deg | 13.539 |
r_dihedral_angle_1_deg | 5.718 |
r_angle_refined_deg | 1.799 |
r_angle_other_deg | 1.049 |
r_chiral_restr | 0.112 |
r_bond_refined_d | 0.017 |
r_gen_planes_refined | 0.01 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7712 |
Nucleic Acid Atoms | |
Solvent Atoms | 495 |
Heterogen Atoms | 206 |
Software
Software | |
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Software Name | Purpose |
HKL-3000 | data collection |
HKL-3000 | phasing |
MOLREP | phasing |
REFMAC | refinement |
Coot | model building |
HKL-3000 | data reduction |
HKL-3000 | data scaling |