2UYB
S161A mutant of Bacillus subtilis Oxalate Decarboxylase OxdC
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 8.5 | 8-15% PEG 8000, 0.1 M TRIS PH8.5, 0-15% XYLITOL | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.2 | 62 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 154.652 | α = 90 |
| b = 154.652 | β = 90 |
| c = 121.892 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | H 3 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 | IMAGE PLATE | MARRESEARCH | OSMIC CONFOCAL MIRRORS | 2004-12-17 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU RUH3R | |||
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 | 2.1 | 31.72 | 100 | 0.14 | 15.28 | 7.76 | 32697 | 13.17 | |||||||||||
| 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 | 2.1 | 2.12 | 99.9 | 0.38 | 5.39 | 7.26 | |||||||||||||
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 1UW8 | 2.1 | 30.18 | 32696 | 1641 | 100 | 0.14 | 0.138 | 0.183 | RANDOM | 12.61 | ||||||
| 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] | |
| -0.703 | -0.351 | -0.703 | 1.054 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 30.358 |
| r_dihedral_angle_4_deg | 19.658 |
| r_dihedral_angle_3_deg | 12.911 |
| r_dihedral_angle_1_deg | 6.604 |
| r_scangle_it | 3.344 |
| r_scbond_it | 2.221 |
| r_angle_refined_deg | 1.438 |
| r_mcangle_it | 1.299 |
| r_mcbond_it | 0.843 |
| r_nbtor_refined | 0.305 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2999 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 412 |
| Heterogen Atoms | 13 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
| REFMAC | phasing |
