X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6OJ1 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 293 | Index A6. 0.1 M Tris 8.5, 2 M ammonium sulphate, with 1 mM TEW, Anderson-Evans polyoxotungstate Jena Bioscience added to the protein prior to crystallisation. Microseed Matrix Seeding | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.06 | 59.86 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 95.569 | α = 90 |
| b = 95.569 | β = 90 |
| c = 231.428 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 31 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 EIGER X 16M | 2019-06-30 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9795 | Diamond | I04 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 1.61 | 82.77 | 100 | 0.113 | 0.123 | 0.049 | 0.999 | 11.2 | 12.2 | 158994 | 20.4 | ||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 1.61 | 1.64 | 100 | 2.346 | 2.563 | 1.027 | 0.461 | 1 | 12.1 | ||||||||||
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-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.61 | 82.765 | 158854 | 8055 | 99.971 | 0.179 | 0.1778 | 0.1778 | 0.1951 | 0.1951 | 29.115 | ||||||
| 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] | |
| 0.315 | 0.158 | 0.315 | -1.022 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_6_deg | 15.272 |
| r_dihedral_angle_3_deg | 11.068 |
| r_dihedral_angle_2_deg | 7.081 |
| r_lrange_it | 6.536 |
| r_lrange_other | 6.394 |
| r_dihedral_angle_1_deg | 6.202 |
| r_scangle_it | 3.955 |
| r_scangle_other | 3.955 |
| r_scbond_it | 2.554 |
| r_scbond_other | 2.554 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 6785 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 993 |
| Heterogen Atoms | 48 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| xia2 | data reduction |
| XDS | data reduction |
| Aimless | data scaling |
| MOLREP | phasing |
| REFMAC | refinement |
