2P4G
CRYSTAL STRUCTURE OF A PYRIMIDINE REDUCTASE-LIKE PROTEIN (DIP1392) FROM CORYNEBACTERIUM DIPHTHERIAE NCTC AT 2.30 A RESOLUTION
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 277 | NANODROP, 0.2M Potassium nitrate, 20.0% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K | |
| 2 | VAPOR DIFFUSION, SITTING DROP | 6.9 | 277 | NANODROP, 0.2M Potassium nitrate, 20.0% PEG 3350, No Buffer pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 113.51 | α = 90 |
| b = 113.51 | β = 90 |
| c = 55.94 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 64 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2006-09-22 | M | SINGLE WAVELENGTH | ||||||
| 2 | 2 | x-ray | 100 | CCD | MARMOSAIC 325 mm CCD | Flat collimating mirror, toroid focusing mirror | 2006-06-18 | M | MAD | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ALS BEAMLINE 5.0.3 | 1.00000 | ALS | 5.0.3 |
| 2 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.97922, 0.97939, 0.91162 | SSRL | BL9-2 |
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 | 2.3 | 28.273 | 97.3 | 0.052 | 11.61 | 3.66 | 18260 | 46.09 | |||||||||||
| 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 | 2.3 | 2.38 | 92.9 | 0.41 | 1.76 | ||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MAD | THROUGHOUT | 2.3 | 28.273 | 18113 | 922 | 98.39 | 0.175 | 0.175 | 0.173 | 0.225 | RANDOM | 60.7 | ||||||
| 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] | |
| 0.08 | 0.04 | 0.08 | -0.12 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.576 |
| r_dihedral_angle_4_deg | 18.875 |
| r_dihedral_angle_3_deg | 13.499 |
| r_dihedral_angle_1_deg | 7.053 |
| r_scangle_it | 6.955 |
| r_scbond_it | 5.366 |
| r_mcangle_it | 2.897 |
| r_mcbond_it | 1.742 |
| r_angle_refined_deg | 1.449 |
| r_angle_other_deg | 0.926 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1846 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 113 |
| Heterogen Atoms | 64 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| MolProbity | model building |
| SOLVE | phasing |
| REFMAC | refinement |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| ADSC | data collection |
| XDS | data reduction |
