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Crystal structure of human K-Ras G12D Mutant in complex with GDP and Cyclic Inhibitory Peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QL3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1M Hepes, 50% PEG 200
Crystal Properties Matthews coefficient Solvent content 2.26 45.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.529 α = 90 b = 51.529 β = 90 c = 129.741 γ = 120
Symmetry Space Group P 31 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 S 6M 2017-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.25 50 100 0.041 54.4 9.3 56366
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.27 99.7 0.964 1.9 7.3
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 4QL3 1.25 44.63 53531 2766 99.91 0.17191 0.17077 0.1795 0.19403 0.199 RANDOM 19.106
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] 0.03 0.02 0.03 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.267 r_dihedral_angle_4_deg 21.743 r_dihedral_angle_3_deg 13.758 r_dihedral_angle_1_deg 6.004 r_long_range_B_refined 3.554 r_long_range_B_other 3.51 r_scangle_other 2.172 r_angle_refined_deg 1.592 r_mcangle_it 1.459 r_mcangle_other 1.454
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.267 r_dihedral_angle_4_deg 21.743 r_dihedral_angle_3_deg 13.758 r_dihedral_angle_1_deg 6.004 r_long_range_B_refined 3.554 r_long_range_B_other 3.51 r_scangle_other 2.172 r_angle_refined_deg 1.592 r_mcangle_it 1.459 r_mcangle_other 1.454 r_scbond_other 1.358 r_scbond_it 1.356 r_angle_other_deg 1.104 r_mcbond_it 0.892 r_mcbond_other 0.873 r_chiral_restr 0.095 r_bond_other_d 0.014 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 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 1539 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing