5XY4
CATPO mutant - V536W
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 4AUM | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 323 | PEG400, Potassium chloride, Calcium chloride, Sodium cacodylate | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.29 | 46.33 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 125.42 | α = 90 |
| b = 120.743 | β = 102.05 |
| c = 184.653 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | I 1 2 1 |
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 6M | 2016-12-16 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID30B | 0.9762 | ESRF | ID30B |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.8 | 100.37 | 90 | 0.054 | 0.047 | 0.998 | 8.8 | 1.9 | 252686 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 1 | 1.8 | 1.83 | 91.1 | 0.52 | 0.455 | 0.643 | 1.6 | 1.8 | |||||||||||
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 | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 4AUM | 1.8 | 90.46 | 211910 | 11268 | 89.86 | 0.15961 | 0.15784 | 0.19297 | RANDOM | 26.712 | ||||||
| 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] | |
| -1.19 | -0.84 | 0.79 | 0.69 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.908 |
| r_dihedral_angle_4_deg | 17.281 |
| r_dihedral_angle_3_deg | 12.678 |
| r_dihedral_angle_1_deg | 7.096 |
| r_long_range_B_refined | 4.594 |
| r_long_range_B_other | 4.594 |
| r_scangle_other | 2.603 |
| r_mcangle_it | 1.92 |
| r_mcangle_other | 1.92 |
| r_angle_refined_deg | 1.78 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 21153 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 2030 |
| Heterogen Atoms | 193 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| MOLREP | phasing |
| Aimless | data scaling |
