6ZL5
CRYSTAL STRUCTURE OF KRAS-G12D(C118S) IN COMPLEX WITH BI-2852 AND GDP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6GJ8 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 278 | 2M Ammonium sulfate 100mM Sodium cacodylate 200mM Sodium cloride |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.13 | 70.25 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 83.802 | α = 90 |
b = 83.802 | β = 90 |
c = 87.416 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | RIGAKU SATURN 944 | 2017-04-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | RIGAKU MICROMAX-003 | 1.541800 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | 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 | 1.765 | 60.49 | 92.3 | 0.153 | 0.153 | 22.2 | 17 | 28821 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.765 | 1.771 | 60.7 | 1.158 | 1.158 | 2 | 8.2 |
Refinement
Statistics | |||||||||||||||||||
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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 | 6GJ8 | 1.645 | 60.49 | 31182 | 1556 | 81.2 | 0.1967 | 0.1961 | 0.2093 | RANDOM | 17.37 |
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] | |
0.3027 | 0.3027 | -0.6054 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
t_other_torsion | 15.03 |
t_omega_torsion | 3.38 |
t_angle_deg | 0.84 |
t_bond_d | 0.008 |
t_dihedral_angle_d | |
t_gen_planes | |
t_it | |
t_chiral_improper_torsion | |
t_ideal_dist_contact |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1301 |
Nucleic Acid Atoms | |
Solvent Atoms | 183 |
Heterogen Atoms | 73 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
autoPROC | data reduction |
XDS | data reduction |
autoPROC | data scaling |
Aimless | data scaling |
PHASER | phasing |