7P0C
URATE OXIDASE WITH 8-AZAXANTHINE UNDER 210 MPA PRESSURE
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 4OP9 | PDB 4OP9 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 7.5 | 298 | 20 MG/ML URATE OXIDASE, 8-AZAXANTHINE CONCENTRATION IN EXCESS, 50 MM TRIS/ACETATE, 8% PEG 4000 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.91 | 57.78 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 79.53 | α = 90 |
b = 95.63 | β = 90 |
c = 104.754 | γ = 90 |
Symmetry | |
---|---|
Space Group | I 2 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 293 | CCD | RAYONIX SX-165mm | mirrors | 2019-07-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SOLEIL BEAMLINE CRISTAL | 0.58183 | SOLEIL | CRISTAL |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.15 | 29.588 | 96 | 0.174 | 5.6 | 3.3 | 21075 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.15 | 2.27 | 97.1 | 0.701 | 0.701 | 1 | 3.3 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 4OP9 | 2.15 | 20 | 17795 | 944 | 84.77 | 0.1924 | 0.1893 | 0.2479 | RANDOM | 28.891 |
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] | |
2.55 | -0.71 | -1.84 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.021 |
r_dihedral_angle_3_deg | 14.192 |
r_dihedral_angle_4_deg | 13.286 |
r_dihedral_angle_1_deg | 7.019 |
r_angle_refined_deg | 1.659 |
r_angle_other_deg | 0.977 |
r_chiral_restr | 0.093 |
r_bond_refined_d | 0.014 |
r_gen_planes_refined | 0.008 |
r_gen_planes_other | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2362 |
Nucleic Acid Atoms | |
Solvent Atoms | 180 |
Heterogen Atoms | 23 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
MOLREP | phasing |
PDB_EXTRACT | data extraction |