2W0U
CRYSTAL STRUCTURE OF HUMAN GLYCOLATE OXIDASE IN COMPLEX WITH THE INHIBITOR 5-[(4-CHLOROPHENYL)SULFANYL]- 1,2,3-THIADIAZOLE-4-CARBOXYLATE.
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2NZL | PDB ENTRY 2NZL |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | CRYSTALLISATION WAS PERFORMED BY THE HANGING DROP VAPOR DIFFUSION METHOD, USING A PRECIPITANT SOLUTION CONTAINING 200 MM NACL, 100 MM MMT AT PH 7.5, AND 15% (W/V) POLYETHYLENE GLYCOL 1000 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.07 | 59.62 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 138.69 | α = 90 |
| b = 138.69 | β = 90 |
| c = 186.84 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 4 21 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 110 | CCD | ADSC CCD | 2007-08-26 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-3 | ESRF | ID14-3 | |
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 | 2.8 | 47.4 | 100 | 0.09 | 7 | 43574 | 2 | ||||||||||||
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 ENTRY 2NZL | 2.84 | 46.73 | 41393 | 2179 | 100 | 0.207 | 0.205 | 0.25 | RANDOM | 38.1 | ||||||
| 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] | |
| -0.18 | -0.18 | 0.35 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.126 |
| r_dihedral_angle_3_deg | 17.131 |
| r_dihedral_angle_4_deg | 16.628 |
| r_dihedral_angle_1_deg | 5.639 |
| r_scangle_it | 1.744 |
| r_angle_refined_deg | 1.182 |
| r_scbond_it | 1.109 |
| r_mcangle_it | 0.844 |
| r_mcbond_it | 0.652 |
| r_nbtor_refined | 0.302 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 10344 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 33 |
| Heterogen Atoms | 188 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| SCALA | data scaling |
| MOLREP | phasing |
