5F2E

Crystal Structure of small molecule ARS-853 covalently bound to K-Ras G12C


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LUC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP10.52932.2 M 3:2 NaH2PO4/K2HPO4, 0.2 M Li2SO4, 0.1 M glycine pH=10.5
Crystal Properties
Matthews coefficientSolvent content
2.0539.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.11α = 90
b = 43.08β = 90
c = 93.96γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-04-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.977408ALS5.0.1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.446.9897.60.0630.0730.03512.543126131261
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4885.60.3070.3070.2152.52.93855

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4LUC1.446.9829624158397.370.15160.15030.1759RANDOM13.079
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]
0.03-0.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.242
r_dihedral_angle_4_deg14.471
r_dihedral_angle_3_deg12.496
r_dihedral_angle_1_deg6.906
r_angle_refined_deg2.626
r_mcangle_it1.739
r_mcbond_it1.117
r_angle_other_deg1.111
r_mcbond_other1.104
r_chiral_restr0.158
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.242
r_dihedral_angle_4_deg14.471
r_dihedral_angle_3_deg12.496
r_dihedral_angle_1_deg6.906
r_angle_refined_deg2.626
r_mcangle_it1.739
r_mcbond_it1.117
r_angle_other_deg1.111
r_mcbond_other1.104
r_chiral_restr0.158
r_bond_refined_d0.025
r_gen_planes_refined0.017
r_gen_planes_other0.006
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1336
Nucleic Acid Atoms
Solvent Atoms187
Heterogen Atoms81

Software

Software
Software NamePurpose
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction