6P8Z
Crystal structure of human KRAS G12C covalently bound to an acryloylazetidine acetamide inhibitor
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 293 | 0.2M Calcium chloride, 0.1M TRIS pH8.5, 20% PEG 4000 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.87 | 34.12 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 39.758 | α = 90 |
| b = 65.392 | β = 105.09 |
| c = 62.596 | 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 | CCD | ADSC QUANTUM 315r | 2016-09-23 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ALS BEAMLINE 5.0.1 | 0.9774 | ALS | 5.0.1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.65 | 30 | 98.7 | 0.108 | 0.13 | 0.071 | 7.1 | 3.4 | 37138 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 1.65 | 1.71 | 99.8 | 0.613 | 0.724 | 0.382 | 0.829 | 1.55 | 3.5 | ||||||||||
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1.65 | 30 | 34850 | 1774 | 98.11 | 0.23126 | 0.22933 | 0.2693 | RANDOM | 32.301 | |||||||
| 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] | |
| 3.6 | -0.41 | -0.02 | -2.93 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 38.064 |
| r_dihedral_angle_4_deg | 17.605 |
| r_dihedral_angle_3_deg | 14.818 |
| r_dihedral_angle_1_deg | 4.877 |
| r_long_range_B_refined | 4.348 |
| r_long_range_B_other | 4.195 |
| r_scangle_other | 2.026 |
| r_mcangle_it | 1.94 |
| r_mcangle_other | 1.939 |
| r_mcbond_it | 1.243 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2641 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 255 |
| Heterogen Atoms | 140 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| DENZO | data reduction |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| HKL-2000 | data scaling |
| PHASER | phasing |
| REFMAC | refinement |
| Coot | model building |
