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Human K-Ras G12D (GDP-bound) in complex with cyclic peptide inhibitor AP8784
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Ammonium iodide, 20.0 %w/v Polyethylene glycol 3,350, and 25%v/v Ethylene glycol as a cryoprotectant
Crystal Properties Matthews coefficient Solvent content 2.49 50.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.012 α = 90 b = 66.012 β = 90 c = 86.33 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 EIGER X 16M 2021-09-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000006 SLS X10SA
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 1.878 34.45 94 0.0505 0.052 0.0121 0.999 23.58 19.28 12671
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) 1.878 2.079 69.1 1.8302 1.8843 0.4417 0.664 1.53 18.05 636
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.878 34.45 12671 623 69.4 0.2611 0.2589 0.2511 0.2985 0.2936 RANDOM 56.01
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] 0.1406 0.1406 -0.2813
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.57 t_omega_torsion 3.1 t_angle_deg 0.93 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 16.57 t_omega_torsion 3.1 t_angle_deg 0.93 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 1409 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 35
Software Software Software Name Purpose BUSTER refinement autoPROC data processing XDS data reduction Aimless data scaling STARANISO data scaling PHASER phasing