9USB | pdb_00009usb

GppNHp-bound KRAS G12D in complex with MCB-294


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7EW9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52980.2 M sodium acetate, 0.1 M Tris, pH 8.5, 26% (w/v) PEG 3350.
Crystal Properties
Matthews coefficientSolvent content
2.244.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.184α = 90
b = 102.574β = 107.19
c = 56.362γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002025-04-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A11NSRRCBL15A1

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
12.352598.50.06616.523.621662
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)
12.352.430.339

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 REPLACEMENTTHROUGHOUT2.3523.8120582105996.20.176340.173010.18760.242260.2541RANDOM50.613
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]
5.442.35-4.43-2.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.659
r_dihedral_angle_4_deg19.076
r_dihedral_angle_3_deg15.956
r_long_range_B_other9.282
r_long_range_B_refined9.281
r_dihedral_angle_1_deg7.291
r_scangle_other7.244
r_mcangle_other6.195
r_mcangle_it6.194
r_scbond_other4.923
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.659
r_dihedral_angle_4_deg19.076
r_dihedral_angle_3_deg15.956
r_long_range_B_other9.282
r_long_range_B_refined9.281
r_dihedral_angle_1_deg7.291
r_scangle_other7.244
r_mcangle_other6.195
r_mcangle_it6.194
r_scbond_other4.923
r_scbond_it4.921
r_mcbond_it4.286
r_mcbond_other4.28
r_angle_refined_deg1.91
r_angle_other_deg1.294
r_chiral_restr0.067
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.002
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 Atoms3997
Nucleic Acid Atoms
Solvent Atoms74
Heterogen Atoms237

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SAINTdata reduction
SAINTdata scaling
PHASERphasing