9E9H | pdb_00009e9h

Crystal structure of human KRAS G12C covalently bound to DEL triazine compound 5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6OIM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.001M calcium chloride, 0.1M MES pH6.5, 30% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
1.9436.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.715α = 90
b = 40.715β = 90
c = 341.304γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-02-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.00000APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.653091.90.0480.99812.343.534847
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.7568.50.4610.8611.963.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.65301882695591.270.210660.208710.21920.249890.2545RANDOM35.819
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]
1.120.561.12-3.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.658
r_dihedral_angle_4_deg20.116
r_dihedral_angle_3_deg13.711
r_dihedral_angle_1_deg4.775
r_long_range_B_refined4.438
r_long_range_B_other4.397
r_scangle_other2.923
r_mcangle_it2.268
r_mcangle_other2.267
r_scbond_it1.748
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.658
r_dihedral_angle_4_deg20.116
r_dihedral_angle_3_deg13.711
r_dihedral_angle_1_deg4.775
r_long_range_B_refined4.438
r_long_range_B_other4.397
r_scangle_other2.923
r_mcangle_it2.268
r_mcangle_other2.267
r_scbond_it1.748
r_scbond_other1.747
r_mcbond_it1.382
r_mcbond_other1.376
r_angle_refined_deg1.176
r_angle_other_deg0.679
r_chiral_restr0.064
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1351
Nucleic Acid Atoms
Solvent Atoms93
Heterogen Atoms70

Software

Software
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
REFMACrefinement
Cootmodel building