9C43 | pdb_00009c43

Crystal structure of GDP-bound KRAS E3K/G12D: Suppressing G12D oncogenicity via second-site E3K mutation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5US4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2932.2 M (NH4)2SO4; 0.2 NH4NO3
Crystal Properties
Matthews coefficientSolvent content
2.2745.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.17α = 90
b = 85.17β = 90
c = 42.03γ = 120
Symmetry
Space GroupP 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-11-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.9791APS24-ID-E

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.8718.9998.60.1280.1380.9919.5727828
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.871.920.57100000000000010.6120.7120000000000001

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5US41.8718.9926535129298.690.132530.131210.13280.159790.1599RANDOM31.266
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]
-4.98-4.989.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.673
r_dihedral_angle_1_deg6.186
r_long_range_B_refined5.645
r_long_range_B_other5.502
r_dihedral_angle_2_deg3.418
r_scangle_other3.251
r_mcangle_it2.598
r_scbond_it2.007
r_scbond_other2.001
r_mcbond_it1.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.673
r_dihedral_angle_1_deg6.186
r_long_range_B_refined5.645
r_long_range_B_other5.502
r_dihedral_angle_2_deg3.418
r_scangle_other3.251
r_mcangle_it2.598
r_scbond_it2.007
r_scbond_other2.001
r_mcbond_it1.63
r_angle_refined_deg1.052
r_angle_other_deg0.317
r_chiral_restr0.079
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_bond_other_d
r_dihedral_angle_4_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2635
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms63

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing