4RV4
2.65 Angstrom Resolution Crystal Structure of an orotate phosphoribosyltransferase from Bacillus anthracis str. 'Ames Ancestor' in complex with 5-phospho-alpha-D-ribosyl diphosphate (PRPP)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3M3H | PDB ID 3M3H |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4 | 295 | 7 MG/ML PROTEIN IN 10 MM TRIS/HCL PH 8.0, 500 MM NACL, 5 MM BME, 10 MM 5-PHOSPHO-ALPHA-D-RIBOSYL DIPHOSPHATE (PRPP). CRYSTALS GREW FROM 0.1 M MIB BUFFER PH 4.0, 25% (W/V) PEG1500 (THE PACT SUITE CONDITION #13), VAPOR DIFFUSION, SITTING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 44.02 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 133.268 | α = 90 |
b = 133.268 | β = 90 |
c = 151.348 | γ = 90 |
Symmetry | |
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Space Group | I 4 2 2 |
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/Diamond Laue Mono | 2010-08-19 | 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) | 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 | 2.65 | 30 | 90 | 0.066 | 20.82 | 6.6 | 18197 | 18197 | -3 | 64.9 |
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) | |||||||||||
1 | 2.65 | 2.7 | 97.7 | 0.49 | 4.3 | 6.6 | 983 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 ID 3M3H | 2.65 | 29.54 | 17278 | 919 | 89.85 | 0.19814 | 0.19581 | 0.24181 | RANDOM | 75.808 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-5.39 | -5.39 | 10.78 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 25.542 |
r_dihedral_angle_4_deg | 15.348 |
r_dihedral_angle_3_deg | 9.296 |
r_dihedral_angle_1_deg | 1.923 |
r_angle_refined_deg | 1.645 |
r_angle_other_deg | 1.128 |
r_chiral_restr | 0.096 |
r_bond_refined_d | 0.011 |
r_gen_planes_refined | 0.007 |
r_bond_other_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4693 |
Nucleic Acid Atoms | |
Solvent Atoms | 35 |
Heterogen Atoms | 73 |
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 |