6IC1
urate oxidase under 90 bar of krypton
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1R51 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | BATCH MODE | 8 | 291 | 20 MicroL URATE OXIDASE (at 20 mg/ML+0.2MG/ML 8-AZAXANTHINE, 50mM TRIS) MIXED WIH 20 microL (TRIS + PEG 8000 4-8%). |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.96 | 57.8 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 79.47 | α = 90 |
| b = 94.939 | β = 90 |
| c = 104.098 | 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 | 100 | PIXEL | DECTRIS PILATUS3 S 6M | 2017-06-14 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE BM30A | 0.999 | ESRF | BM30A |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 1.1 | 70.15 | 93.1 | 0.056 | 0.063 | 0.028 | 0.999 | 10.1 | 4.7 | 147453 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 1.1 | 1.16 | 90 | 0.46 | 0.516 | 0.231 | 0.879 | 2.4 | 4.8 | ||||||||||
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 | Mean Isotropic B | |||||||
| X-RAY DIFFRACTION | FOURIER SYNTHESIS | NONE | 1R51 | 1.1 | 70.15 | 147342 | 92.84 | 0.11546 | 0.11546 | 15.938 | |||||||||
| 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] | |
| -0.19 | 0.11 | 0.07 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.03 |
| r_dihedral_angle_3_deg | 13.751 |
| r_dihedral_angle_4_deg | 11.701 |
| r_rigid_bond_restr | 8.325 |
| r_dihedral_angle_1_deg | 7.109 |
| r_long_range_B_refined | 4.482 |
| r_long_range_B_other | 3.806 |
| r_scangle_other | 3.751 |
| r_mcbond_it | 3.734 |
| r_scbond_it | 3.718 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2362 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 544 |
| Heterogen Atoms | 34 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| FFT | phasing |
