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Human KRas4A (GMPPNP) in complex with compound 32
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other unreleased crystal structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 24% PEG 3350, 100 mM MgCl2, 10 mM CoCl2, 100 mM HEPES
Crystal Properties Matthews coefficient Solvent content 2.06 40.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.037 α = 90 b = 34.23 β = 109.71 c = 69.527 γ = 90
Symmetry Space Group C 1 2 1
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 16M 2020-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.57 28.92 98.6 0.028 0.033 0.018 1 20.3 3.3 22125
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 1.57 1.61 88 0.515 0.633 0.361 0.923 2.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.57 28.92 20987 1068 98.2 0.214 0.2127 0.2403 0.253 RANDOM 41.479
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] -0.55 0.94 2.92 -2.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.276 r_dihedral_angle_3_deg 14.155 r_dihedral_angle_4_deg 13.064 r_dihedral_angle_1_deg 4.226 r_mcangle_it 2.389 r_angle_other_deg 2.339 r_angle_refined_deg 1.683 r_mcbond_it 1.582 r_mcbond_other 1.571 r_chiral_restr 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.276 r_dihedral_angle_3_deg 14.155 r_dihedral_angle_4_deg 13.064 r_dihedral_angle_1_deg 4.226 r_mcangle_it 2.389 r_angle_other_deg 2.339 r_angle_refined_deg 1.683 r_mcbond_it 1.582 r_mcbond_other 1.571 r_chiral_restr 0.127 r_bond_other_d 0.035 r_bond_refined_d 0.019 r_gen_planes_other 0.009 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1293 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction