Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 4JX3 | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION | 7.5 | 277 | Na.HEPES, NaCl |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.97 | 58.6 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 97.673 | α = 90 |
| b = 97.673 | β = 90 |
| c = 80.499 | γ = 120 |
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 80 | CCD | ADSC QUANTUM 315r | | 2020-03-13 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | NSRRC BEAMLINE BL13B1 | 1 | NSRRC | BL13B1 |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.14 | 30 | 100 | 0.062 | 0.065 | 0.02 | 14 | 11 | | 24119 | | | 47.17 |
| 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 | 2.14 | 2.22 | 100 | | 1.067 | 1.125 | 0.356 | 0.861 | | 9.9 | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | 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 | THROUGHOUT | 2.141 | 25.034 | 1.34 | 24067 | 2010 | 99.87 | 0.1983 | 0.1963 | 0.197 | 0.2202 | 0.221 | 53.9163 |
| 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 | 5.503 |
| f_angle_d | 1.158 |
| f_chiral_restr | 0.077 |
| f_bond_d | 0.011 |
| f_plane_restr | 0.006 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 2200 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 67 |
| Heterogen Atoms | |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHENIX | phasing |
