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Crystal structure of KRas G12D (GDP) in complex with ASP3082
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7YCC experimental model PDB 6GMR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 296 bis-tris propane, sodium formate, PEG3350
Crystal Properties Matthews coefficient Solvent content 2.75 55.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.348 α = 90 b = 58.905 β = 104.3 c = 165.979 γ = 90
Symmetry Space Group P 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 90 PIXEL DECTRIS EIGER2 XE 16M 2023-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.99999 SPring-8 BL41XU
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 3.18 58.9 100 0.045 0.064 0.045 0.998 10 1.9 46338
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 3.18 3.29 100 0.272 0.385 0.272 0.932 1.9
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 7YCC,6GMR 3.18 48.76 43994 2333 99.92 0.24451 0.2413 0.2482 0.30537 0.3083 RANDOM 140.972
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] -3.42 11.61 -9.25 5.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.204 r_dihedral_angle_3_deg 21.752 r_long_range_B_refined 18.656 r_dihedral_angle_4_deg 17.52 r_mcangle_it 11.51 r_scbond_it 7.548 r_mcbond_it 7.079 r_dihedral_angle_1_deg 7.072 r_angle_refined_deg 1.103 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.204 r_dihedral_angle_3_deg 21.752 r_long_range_B_refined 18.656 r_dihedral_angle_4_deg 17.52 r_mcangle_it 11.51 r_scbond_it 7.548 r_mcbond_it 7.079 r_dihedral_angle_1_deg 7.072 r_angle_refined_deg 1.103 r_chiral_restr 0.083 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16069 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 440
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing