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Human KRas4A (GMPPNP) in complex with compound 36
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, 150 mM MgCl2, 10 mM CoCl2, 100 mM HEPES
Crystal Properties Matthews coefficient Solvent content 2.08 40.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.467 α = 90 b = 34.281 β = 109.29 c = 69.591 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 PILATUS3 6M 2021-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 1.00 Diamond I24
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 1.35 29.5 97.6 0.047 0.057 0.031 0.997 10.3 3 34806
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 1.35 1.39 78.6 0.469 0.587 0.349 0.891 2.4
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 1.35 29.5 33076 1729 97.48 0.1838 0.1821 0.2169 0.2505 RANDOM 30.23
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] 2.85 0.36 0.82 -3.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.953 r_dihedral_angle_3_deg 13.933 r_dihedral_angle_4_deg 10.887 r_dihedral_angle_1_deg 3.795 r_rigid_bond_restr 3.515 r_mcangle_it 2.352 r_angle_other_deg 2.31 r_mcbond_it 1.985 r_mcbond_other 1.976 r_angle_refined_deg 1.703
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.953 r_dihedral_angle_3_deg 13.933 r_dihedral_angle_4_deg 10.887 r_dihedral_angle_1_deg 3.795 r_rigid_bond_restr 3.515 r_mcangle_it 2.352 r_angle_other_deg 2.31 r_mcbond_it 1.985 r_mcbond_other 1.976 r_angle_refined_deg 1.703 r_chiral_restr 0.115 r_bond_other_d 0.034 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_gen_planes_other 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1253 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction