4D82
Metallosphera sedula Vps4 crystal structure
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 5.6 | 1,4 M SODIUM/POTASSIUM PHOSPHATE PH 5.6 (1.26 M SODIUM DIHYDROGEN PHOSPHATE MONOHYDRATE AND 0.14 M DI-POTASSIUM HYDROGEN PHOSPHATE) AND 7.5% (V/V) GLYCEROL | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.09 | 60.25 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 151.187 | α = 90 |
| b = 151.187 | β = 90 |
| c = 98.59 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 65 |
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 | MARMOSAIC 225 mm CCD | 2014-01-29 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | ESRF | ID23-2 | |
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 | 3.2 | 130.9 | 99.6 | 0.14 | 9.9 | 4.6 | 21217 | 2 | |||||||||||
| 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 | 3.2 | 3.4 | 99.8 | 0.51 | 3.1 | 4.7 | |||||||||||||
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 4D81 | 3.2 | 130.93 | 20131 | 1081 | 99.52 | 0.22961 | 0.22755 | 0.26846 | RANDOM | 54.462 | ||||||
| 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] | |
| 1.73 | 0.87 | 1.73 | -5.63 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.403 |
| r_dihedral_angle_4_deg | 20.852 |
| r_dihedral_angle_3_deg | 16.852 |
| r_dihedral_angle_1_deg | 6.504 |
| r_mcangle_it | 3.344 |
| r_scangle_it | 2.866 |
| r_mcbond_other | 1.93 |
| r_mcbond_it | 1.929 |
| r_scbond_it | 1.635 |
| r_angle_refined_deg | 1.549 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 6520 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 12 |
| Heterogen Atoms | 81 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| SCALA | data scaling |
| PHASER | phasing |
