3CLU
Crystal structure of the R236K mutant from Methylophilus methylotrophus ETF
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1O97 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION | 6.2 | limited digest with trypsin, 2.0 M sodium phosphate, pH 6.2, VAPOR DIFFUSION | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.63 | 53.31 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 116.482 | α = 90 |
| b = 116.482 | β = 90 |
| c = 84.281 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 61 |
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 210 | 2005-04-01 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | ESRF | ID14-1 | |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.8 | 19 | 99 | 0.067 | 9.2 | 4.2 | 58203 | 58203 | |||||||||||
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 | FOURIER SYNTHESIS | THROUGHOUT | 1O97 | 1.8 | 19 | 52470 | 2793 | 92.45 | 0.16963 | 0.1678 | 0.20395 | RANDOM | 31.954 | ||||||
| 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] | |
| 1.42 | 0.71 | 1.42 | -2.13 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.046 |
| r_dihedral_angle_4_deg | 20.607 |
| r_dihedral_angle_3_deg | 13.776 |
| r_dihedral_angle_1_deg | 6.373 |
| r_scangle_it | 3.037 |
| r_scbond_it | 1.968 |
| r_angle_refined_deg | 1.541 |
| r_mcangle_it | 1.19 |
| r_angle_other_deg | 0.825 |
| r_mcbond_it | 0.815 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4213 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 544 |
| Heterogen Atoms | 76 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| ADSC | data collection |
| DENZO | data reduction |
| SCALEPACK | data scaling |
