8Q1S
Pathogenic mutations of human phosphorylation sites affect protein-protein interactions
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2WH0 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 293 | 19% PEG 3350, 0.35 M NaBr, 0.1 M BisTris-Propane pH 6.5 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.97 | 58.65 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 123.78 | α = 90 |
| b = 123.78 | β = 90 |
| c = 250.2 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | H 3 2 |
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 PILATUS3 6M | 2022-12-06 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.9184 | BESSY | 14.1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim 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 | 3.23 | 49.7 | 99.9 | 0.035 | 0.995 | 6.91 | 10.39 | 22972 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 3.23 | 3.42 | 0.296 | 0.368 | |||||||||||||||
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 (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3.23 | 49.7 | 11549 | 608 | 99.93 | 0.23286 | 0.23036 | 0.23 | 0.27937 | 0.28 | RANDOM | 122.895 | |||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
| 15.92 | 15.92 | -31.83 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 26.475 |
| r_dihedral_angle_3_deg | 14.191 |
| r_dihedral_angle_4_deg | 11.037 |
| r_long_range_B_other | 5.065 |
| r_long_range_B_refined | 5.062 |
| r_dihedral_angle_1_deg | 4.48 |
| r_mcangle_other | 3.098 |
| r_mcangle_it | 3.097 |
| r_scangle_other | 2.444 |
| r_mcbond_it | 1.766 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3908 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 12 |
| Heterogen Atoms | 10 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XSCALE | data scaling |
| XDS | data reduction |
| PHASER | phasing |
