2B4G
dihydroorotate dehydrogenase
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1JUE | PDB accession code 1JUE |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4 | 298 | 0.4 ul protein 14.1 mg/ml 0.4 ul crystallization buffer, 40% PEG 1000, 0.1M Na Citrate, 0.1M KBr, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2 | 36.9 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 81.605 | ¦Á = 90 |
b = 162.63 | ¦Â = 90 |
c = 163.07 | ¦Ã = 90 |
Symmetry | |
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Space Group | C 2 2 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 | ADSC QUANTUM 210 | 2005-09-05 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.1 | 0.9201 | ALS | 8.2.1 |
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 | 1.95 | 163 | 96.2 | 0.107 | 0.107 | 6 | 4.4 | 76097 |
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 | 1.95 | 2.06 | 0.428 | 0.428 | 1.8 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB accession code 1JUE | 1.95 | 50 | 75972 | 72158 | 3814 | 96 | 0.1916 | 0.18894 | 0.24243 | RANDOM | 14.022 |
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] | |
-0.78 | 1.08 | -0.3 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.521 |
r_dihedral_angle_4_deg | 15.886 |
r_dihedral_angle_3_deg | 13.928 |
r_dihedral_angle_1_deg | 6.255 |
r_scangle_it | 2.256 |
r_scbond_it | 1.495 |
r_angle_refined_deg | 1.326 |
r_angle_other_deg | 0.837 |
r_mcangle_it | 0.821 |
r_mcbond_it | 0.714 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9572 |
Nucleic Acid Atoms | |
Solvent Atoms | 638 |
Heterogen Atoms | 203 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
PDB_EXTRACT | data extraction |
REFMAC | refinement |
CCP4 | data scaling |
MOLREP | phasing |