7M0M
HPK1 IN COMPLEX WITH COMPOUND 1
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION | 293 | 20 mM Tris pH 8.0 , 150 mM NaCl , 5% Glycerol , 2 mM DTT | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.58 | 52.33 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 51.168 | α = 86.73 |
| b = 56.994 | β = 86.63 |
| c = 63.459 | γ = 67.06 |
| Symmetry | |
|---|---|
| Space Group | P 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 PILATUS 6M | 2019-08-06 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.97625 | Diamond | I03 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (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 | 1.93 | 63.31 | 97.3 | 0.039 | 0.051 | 0.999 | 13.66 | 2.2 | 48216 | 41.083 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 1 | 1.93 | 2.18 | 96.1 | 0.442 | 0.576 | 1 | 2.52 | 2.3 | |||||||||||
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 | PREVIOUSLY SOLVED STRUCTURE | 1.93 | 63.31 | 46005 | 2211 | 97.33 | 0.1877 | 0.1861 | 0.2198 | RANDOM | 46.723 | ||||||
| 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] | |
| 1.29 | 0.48 | -1.53 | -0.86 | 0.49 | 0.18 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.615 |
| r_dihedral_angle_4_deg | 21.62 |
| r_dihedral_angle_3_deg | 12.714 |
| r_dihedral_angle_1_deg | 6.277 |
| r_angle_refined_deg | 1.587 |
| r_angle_other_deg | 1.266 |
| r_chiral_restr | 0.092 |
| r_bond_refined_d | 0.011 |
| r_gen_planes_refined | 0.007 |
| r_bond_other_d | 0.003 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4611 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 350 |
| Heterogen Atoms | 70 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| XSCALE | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| REFMAC | phasing |
