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Crystal structure of KRas G12D (GDP) in complex with compound 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7YCC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 296 Tris, magnesium chloride, NaCl, PEG3350
Crystal Properties Matthews coefficient Solvent content 2.29 46.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.936 α = 90 b = 67.936 β = 90 c = 200.1 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 PIXEL DECTRIS PILATUS 2M-F 2022-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.36 38.11 99.9 0.073 0.078 0.026 0.998 20.4 9.3 38647
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.36 1.38 99.9 0.967 1.027 0.341 0.801 9.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7YCC 1.36 38.11 36710 1878 99.76 0.22379 0.22271 0.2227 0.24534 0.2455 RANDOM 18.215
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] -0.3 -0.15 -0.3 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.255 r_dihedral_angle_4_deg 13.993 r_dihedral_angle_3_deg 12.916 r_dihedral_angle_1_deg 6.5 r_long_range_B_refined 5.07 r_scbond_it 2.854 r_mcangle_it 2.414 r_angle_refined_deg 2.038 r_mcbond_it 1.656 r_chiral_restr 0.142
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.255 r_dihedral_angle_4_deg 13.993 r_dihedral_angle_3_deg 12.916 r_dihedral_angle_1_deg 6.5 r_long_range_B_refined 5.07 r_scbond_it 2.854 r_mcangle_it 2.414 r_angle_refined_deg 2.038 r_mcbond_it 1.656 r_chiral_restr 0.142 r_gen_planes_refined 0.016 r_bond_refined_d 0.011 r_bond_other_d r_angle_other_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_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1336 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing