7BJJ
Crystal structure of CHK1-10pt-mutant complex with compound 9
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 5OOP | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | 7% PEG 8000, 0.1 M MES buffer pH 6.5, 20% ethylene glycol |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.34 | 47.34 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 45.219 | α = 90 |
| b = 65.926 | β = 101.5 |
| c = 54.526 | 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 EIGER2 XE 16M | 2020-09-29 | 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) | 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 | 1.74 | 53.4 | 74.6 | 0.043 | 0.999 | 8 | 3 | 24286 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 1.74 | 1.87 | 19.2 | 0.626 | 0.65 | 1.6 | 3.1 | ||||||||||||
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 | 5oop | 1.8 | 25 | 22796 | 1193 | 82.14 | 0.1731 | 0.1717 | 0.1993 | RANDOM | 41.891 | ||||||
| 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] | |
| -0.31 | 0.08 | 0.1 | 0.17 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.273 |
| r_dihedral_angle_3_deg | 15.788 |
| r_dihedral_angle_4_deg | 15.176 |
| r_dihedral_angle_1_deg | 6.337 |
| r_angle_refined_deg | 1.632 |
| r_angle_other_deg | 1.333 |
| r_chiral_restr | 0.076 |
| r_bond_refined_d | 0.01 |
| r_gen_planes_refined | 0.009 |
| r_bond_other_d | 0.001 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2077 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 199 |
| Heterogen Atoms | 11 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| XDS | data reduction |
| XSCALE | data scaling |
| MOLREP | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
