4YRW
rat xanthine oxidoreductase, C-terminal deletion protein variant
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1WYG |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | PEG 8000, lithium formate, DTT, sodium salicylate, EDTA, glycerol, HEPES |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.67 | 53.88 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 98.497 | α = 90 |
b = 138.468 | β = 90 |
c = 222.213 | 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 | ADSC QUANTUM 210r | 2007-10-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NW12A | 1 | Photon Factory | AR-NW12A |
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 | 1.99 | 50 | 99.5 | 0.06 | 15.1 | 3.7 | 206697 |
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 | 1.99 | 2.06 | 96.4 | 0.202 | 3.6 | 19848 |
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 | 1WYG | 1.99 | 43.33 | 196212 | 10396 | 99.63 | 0.1883 | 0.1861 | 0.2293 | RANDOM | 29.599 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.363 |
r_dihedral_angle_4_deg | 18.803 |
r_dihedral_angle_3_deg | 16.18 |
r_dihedral_angle_1_deg | 6.83 |
r_mcangle_it | 3.485 |
r_mcbond_it | 2.641 |
r_mcbond_other | 2.64 |
r_angle_refined_deg | 2.068 |
r_angle_other_deg | 0.98 |
r_chiral_restr | 0.151 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 19904 |
Nucleic Acid Atoms | |
Solvent Atoms | 638 |
Heterogen Atoms | 174 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALEPACK | data scaling |
PDB_EXTRACT | data extraction |
SCALEPACK | data reduction |
MOLREP | phasing |