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Human KRas4A (GMPPNP) in complex with compound 34
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 20% PEG 3350, 150 mM MgCl2, 10 mM CoCl2, 100 mM HEPES
Crystal Properties Matthews coefficient Solvent content 2.07 40.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.063 α = 90 b = 34.426 β = 109.45 c = 69.548 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 2021-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97953 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 1.33 26.75 97.1 0.018 0.021 0.011 1 30.2 3.4 36064
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 1.33 1.36 91.7 0.592 0.703 0.375 0.945 3.3
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 1.33 26.75 34264 1800 96.66 0.1979 0.1954 0.2474 0.264 RANDOM 28.303
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] 0.7 -1.8 1.53 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.326 r_dihedral_angle_4_deg 14.614 r_dihedral_angle_3_deg 13.826 r_rigid_bond_restr 11.491 r_dihedral_angle_1_deg 4.449 r_mcangle_it 4.185 r_mcbond_other 3.803 r_mcbond_it 3.796 r_angle_other_deg 2.375 r_angle_refined_deg 1.906
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.326 r_dihedral_angle_4_deg 14.614 r_dihedral_angle_3_deg 13.826 r_rigid_bond_restr 11.491 r_dihedral_angle_1_deg 4.449 r_mcangle_it 4.185 r_mcbond_other 3.803 r_mcbond_it 3.796 r_angle_other_deg 2.375 r_angle_refined_deg 1.906 r_chiral_restr 0.132 r_bond_other_d 0.034 r_bond_refined_d 0.017 r_gen_planes_other 0.013 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1284 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction