Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
in silico model | AlphaFold | | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | EVAPORATION | 7.5 | 293 | 1.4 M sodium citrate |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.07 | 40.62 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 70.886 | α = 90 |
| b = 64.296 | β = 96.37 |
| c = 82.27 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 1 21 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 R 4M | | 2024-07-19 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | SPRING-8 BEAMLINE BL26B1 | 1.00 | SPring-8 | BL26B1 |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.92 | 47.49 | 99 | 0.053 | 0.031 | 0.999 | 12 | 4.5 | | 55743 | | | 35.5 |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 1.92 | 1.97 | | | 0.741 | 0.435 | 0.652 | 1.8 | | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | AlphaFold | 1.92 | 40.88 | 1.34 | 55703 | 2729 | 98.81 | 0.1944 | 0.1918 | 0.1918 | 0.2437 | 0.2438 | |
| 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] |
|---|
| | | | | |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| f_dihedral_angle_d | 16.728 |
| f_angle_d | 0.863 |
| f_chiral_restr | 0.05 |
| f_bond_d | 0.008 |
| f_plane_restr | 0.006 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 6228 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 399 |
| Heterogen Atoms | 46 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| XDS | data scaling |
| XDS | data reduction |
| PHENIX | phasing |
| PDB_EXTRACT | data extraction |
