3UNC
Crystal Structure of Bovine Milk Xanthine Dehydrogenase to 1.65A Resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1FO4 | PBD Entry 1FO4 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | Sitting Drop Batch Slide | 7.5 | 293 | 12 mg/ml Xanthine Dehydrogenase (from Bovine Milk), 8 % Polyethylene Glycol 4000, 30 % Glycerol, 5 mM Dithiothreitol, 0.5 mM Sodium Salicylate, 0.2 m Ethylenediaminetetraacetic Acid, 16.65 mM Sodium Pyrophosphate (pH 8.5), 25 mM Potasium Phosphate (pH 6.5). , Sitting Drop Batch Slide, temperature 293.0K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.63 | 53.16 |
Crystal Data
Unit Cell | |
---|---|
Length ( ? ) | Angle ( ? ) |
a = 167.573 | ¦Á = 90 |
b = 124.37 | ¦Â = 91.02 |
c = 148.177 | ¦Ã = 90 |
Symmetry | |
---|---|
Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 93 | CCD | ADSC QUANTUM 210 | 2001-03-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL44B2 | 1.000 | SPring-8 | BL44B2 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.65 | 20 | 99.9 | 0.053 | 25.5 | 4.3 | 364190 | 363495 | -3 | -3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.65 | 1.67 | 99.9 | 0.454 | 3.8 | 14437 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | shells | PBD Entry 1FO4 | 1.65 | 20 | 363495 | 363267 | 4422 | 0.1772 | 0.1962 | random shells |
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] | |
1.543 | -0.141 | 4.321 | -5.864 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_angle_deg | 1.54787 |
c_bond_d | 0.010757 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 19998 |
Nucleic Acid Atoms | |
Solvent Atoms | 1966 |
Heterogen Atoms | 352 |
Software
Software | |
---|---|
Software Name | Purpose |
CNS | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
CNS | phasing |