4NF2
Crystal structure of anabolic ornithine carbamoyltransferase from Bacillus anthracis 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 | 4H31 | PDB ENTRY 4H31 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 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: Index #79 (0.1 M Bis-Tris pH 6.5, 0.2 M NH4 Acetate,25% w/v PEG 3350). Mixed as 0.2 ul + 0.2 ul., VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.23 | 44.79 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 85.893 | α = 90 |
b = 99.893 | β = 90 |
c = 118.989 | 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 WAVELENGT |
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 | 1.74 | 50 | 99.3 | 0.044 | 0.044 | 12.5 | 3.5 | 105890 | 105149 | -3 | 25.5 |
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 | 1.74 | 1.77 | 99.8 | 0.602 | 0.602 | 2 | 3.4 | 5229 |
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 | PDB ENTRY 4H31 | 1.74 | 29.23 | 105456 | 104782 | 5231 | 99.36 | 0.1466 | 0.1466 | 0.1454 | 0.1701 | RANDOM | 32.3437 |
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] | |
0.36 | -1.41 | 1.05 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.069 |
r_dihedral_angle_4_deg | 14.904 |
r_dihedral_angle_3_deg | 13.616 |
r_dihedral_angle_1_deg | 5.735 |
r_angle_refined_deg | 1.695 |
r_angle_other_deg | 1.278 |
r_chiral_restr | 0.103 |
r_bond_refined_d | 0.017 |
r_gen_planes_refined | 0.011 |
r_bond_other_d | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7212 |
Nucleic Acid Atoms | |
Solvent Atoms | 846 |
Heterogen Atoms | 53 |
Software
Software | |
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Software Name | Purpose |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-3000 | data collection |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
MOLREP | phasing |
HKL-3000 | phasing |
CCP4 | phasing |
Coot | model building |