4KWT
Crystal structure of unliganded anabolic ornithine carbamoyltransferase from Vibrio vulnificus at 1.86 A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4H31 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 289 | Protein: 10 mg/ml in 10 mM Tris-HCl pH 8.3, 60 mM Arginine, 500 mM NaCl and 5 mM b-mercaptoethanol. Crystallization condition: 0.1M Bis-Tris pH 6.5, 23% w/v PEG 3350, 0.2M Lithium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.04 | 39.71 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 77.81 | α = 90 |
b = 82.65 | β = 90 |
c = 150.908 | 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 300 mm CCD | BE-LENSES | 2012-06-21 | 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 | 1.86 | 50 | 98.3 | 0.075 | 0.075 | 35.1 | 5.6 | 82600 | 81196 | -3 | 30.4 |
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 | 1.86 | 1.89 | 99.2 | 0.968 | 0.968 | 2.1 | 5.2 | 4055 |
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 | 4H31 | 1.86 | 35.5 | 82448 | 81046 | 4051 | 98.3 | 0.1613 | 0.1613 | 0.1595 | 0.1952 | RANDOM | 39.7325 |
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] | |
-2.85 | -0.77 | 3.62 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.212 |
r_dihedral_angle_4_deg | 16.963 |
r_dihedral_angle_3_deg | 14.396 |
r_dihedral_angle_1_deg | 5.866 |
r_angle_refined_deg | 1.738 |
r_angle_other_deg | 1.382 |
r_chiral_restr | 0.109 |
r_bond_refined_d | 0.019 |
r_gen_planes_refined | 0.011 |
r_bond_other_d | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7515 |
Nucleic Acid Atoms | |
Solvent Atoms | 487 |
Heterogen Atoms | 11 |
Software
Software | |
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Software Name | Purpose |
SCALEPACK | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-3000 | data collection |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
HKL-3000 | phasing |
CCP4 | phasing |
Coot | model building |