4NMM

Crystal Structure of a G12C Oncogenic Variant of Human KRas Bound to a Novel GDP Competitive Covalent Inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4EPVPDB ENTRY 4EPV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
142770.2M MMT pH4.0, 28% PEG 6,000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
1.9336.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.088α = 90
b = 42.022β = 90
c = 91.159γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152013-06-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-IDAPS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.895099.80.12614.4695.812363223.29
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.931000.8832.0365.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4EPV1.8945.5812363116956150.1860.1840.237RANDOM25.81
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]
-2.463.17-0.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.225
r_dihedral_angle_4_deg20.314
r_dihedral_angle_3_deg12.006
r_long_range_B_refined6.816
r_long_range_B_other6.723
r_scangle_other5.14
r_dihedral_angle_1_deg5.011
r_scbond_other3.259
r_scbond_it3.257
r_mcangle_other2.974
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.225
r_dihedral_angle_4_deg20.314
r_dihedral_angle_3_deg12.006
r_long_range_B_refined6.816
r_long_range_B_other6.723
r_scangle_other5.14
r_dihedral_angle_1_deg5.011
r_scbond_other3.259
r_scbond_it3.257
r_mcangle_other2.974
r_mcangle_it2.963
r_mcbond_it2.152
r_mcbond_other2.108
r_angle_refined_deg1.364
r_angle_other_deg0.768
r_chiral_restr0.075
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.007
r_gen_planes_other0.004
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 Atoms1357
Nucleic Acid Atoms
Solvent Atoms125
Heterogen Atoms35

Software

Software
Software NamePurpose
HKL-3000data collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling