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Human K-Ras G12D (GDP-bound) in complex with cyclic peptide inhibitor LUNA18 and KA30L Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VO2 7VO2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 2.0 %v/v Tacsimate (pH 5.0), 0.1 M tri-Sodium citrate (pH 5.6), 16.0 %w/v Polyethylene glycol 3,350, and 25 %v/v Ethylene glycerol as a cryoprotectant
Crystal Properties Matthews coefficient Solvent content 2.51 50.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.617 α = 90 b = 90.373 β = 90 c = 116.81 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M 2020-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.00000 SPring-8 BL45XU
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 1.454 58.41 90.3 0.1335 0.141 0.0442 0.997 16.42 9.35 97915
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) 1.454 1.535 51.2 1.2844 1.4551 0.6544 0.227 1.55 4.58 4897
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 7VO2 1.454 58.41 97915 4912 80 0.2397 0.2377 0.2331 0.2772 0.2669 RANDOM 15.17
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] 0.5215 -0.2787 -0.2428
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.98 t_omega_torsion 4.02 t_angle_deg 1.01 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.98 t_omega_torsion 4.02 t_angle_deg 1.01 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4715 Nucleic Acid Atoms Solvent Atoms 1072 Heterogen Atoms 32
Software Software Software Name Purpose BUSTER refinement autoPROC data processing XDS data reduction Aimless data scaling STARANISO data scaling PHASER phasing