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The crystal structure of KRAS G12R (GDP bound) in complex with RP03519
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7RPZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20%~30% PEG 8000, 200 mM ammonium acetate, 100 mM Tri-sodium citrate pH 4.2,
Crystal Properties Matthews coefficient Solvent content 2.4 48.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.023 α = 90 b = 52.871 β = 90 c = 88.307 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2023-01-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.34 19.34 91.1 0.999 21.7 12.2 39034
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.34 1.363 0.85
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.34 19.34 37131 1902 91.04 0.21282 0.21171 0.2164 0.23427 0.2336 RANDOM 20.018
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] 0.04 0.46 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.925 r_dihedral_angle_2_deg 10.488 r_dihedral_angle_1_deg 5.902 r_long_range_B_refined 5.354 r_long_range_B_other 5.354 r_scangle_other 4.36 r_scbond_other 2.975 r_scbond_it 2.973 r_mcangle_it 2.613 r_mcangle_other 2.612
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.925 r_dihedral_angle_2_deg 10.488 r_dihedral_angle_1_deg 5.902 r_long_range_B_refined 5.354 r_long_range_B_other 5.354 r_scangle_other 4.36 r_scbond_other 2.975 r_scbond_it 2.973 r_mcangle_it 2.613 r_mcangle_other 2.612 r_angle_refined_deg 1.862 r_mcbond_it 1.858 r_mcbond_other 1.851 r_angle_other_deg 0.61 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 Atoms Number Protein Atoms 1348 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 74
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction autoPROC data reduction autoPROC data scaling PHENIX phasing