8S06
A fragment-based inhibitor of SHP2
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 8 | 293 | 0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.16 | 43.13 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 45.504 | α = 90 |
| b = 213.257 | β = 95.99 |
| c = 55.487 | 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 PILATUS 6M | 2016-02-18 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 0.97625 | ESRF | ID23-1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim 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 | 2.19 | 45.3 | 98 | 0.05 | 13.1 | 3.2 | 52645 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 2.19 | 2.26 | 0.778 | 1.6 | |||||||||||||||
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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
| X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | 2.19 | 45.3 | 50053 | 2670 | 98.22 | 0.18042 | 0.1773 | 0.23838 | RANDOM | 57.935 | |||||||
| 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] | |
| 0.63 | 0.21 | 1.08 | -1.72 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.905 |
| r_dihedral_angle_4_deg | 23.599 |
| r_dihedral_angle_3_deg | 16.694 |
| r_long_range_B_other | 9.572 |
| r_long_range_B_refined | 9.567 |
| r_dihedral_angle_1_deg | 7.039 |
| r_scbond_it | 5.12 |
| r_scbond_other | 5.119 |
| r_mcbond_it | 3.837 |
| r_mcbond_other | 3.837 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 8165 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 368 |
| Heterogen Atoms | 20 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| XDS | data reduction |
| Aimless | data scaling |
