3JZE
1.8 Angstrom resolution crystal structure of dihydroorotase (pyrC) from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2EG6 | PDB entry 2EG6 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 295 | Protein solution: 6.8 mg/mL, 0.25 Sodium chloride, Tris-HCl pH 8.3. Screen solution: PEGs II, condition B10, 0.1M Sodium acetate, 0.1M MES pH 6.5, 30% w/v PEG 2000 MME., VAPOR DIFFUSION, SITTING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.18 | 43.69 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.437 | α = 90 |
b = 79.486 | β = 90.35 |
c = 180.61 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | Beryllium lenses | 2009-07-07 | 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 | 1.8 | 30 | 98.6 | 0.083 | 13 | 3.7 | 130226 | 130226 | -3 | 24.5 |
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 | 1.8 | 1.83 | 97.4 | 0.397 | 2.6 | 3.1 | 6322 |
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 2EG6 | 1.8 | 29.83 | 123600 | 123600 | 6556 | 98.48 | 0.16547 | 0.16547 | 0.16347 | 0.20301 | RANDOM | 16.325 |
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] | |
1.01 | -0.58 | 1.74 | -2.76 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.106 |
r_dihedral_angle_4_deg | 10.515 |
r_dihedral_angle_3_deg | 8.604 |
r_scangle_it | 4.334 |
r_dihedral_angle_1_deg | 2.871 |
r_scbond_it | 2.828 |
r_mcangle_it | 1.673 |
r_angle_refined_deg | 1.516 |
r_mcbond_it | 1.022 |
r_angle_other_deg | 0.888 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10728 |
Nucleic Acid Atoms | |
Solvent Atoms | 1328 |
Heterogen Atoms | 112 |
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 |