☰ Navigation Tabs
GDP-bound KRAS G12D in complex with D5543
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7RT1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 100 mM MES (pH 5.5-6.5), PEG 8000 16-24 % (v/v) and 200 mM calcium acetate
Crystal Properties Matthews coefficient Solvent content 2.46 49.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.4817 α = 90 b = 82.4817 β = 90 c = 96.8325 γ = 120
Symmetry Space Group P 65 2 2
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 300K 2023-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CAMD BEAMLINE GCPCC 0.987 CAMD GCPCC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.6 20.04 97.8383458647 0.998 12.52 1 7149 17.57
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6003 2.8613 0.998
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.60033089206 20.0387970593 1.33544389715 6246 616 97.8383458647 0.251629740492 0.247439931503 0.2501 0.288262637306 0.2959 21.7924959936
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.3253563668 f_angle_d 1.2780529564 f_chiral_restr 0.155528901976 f_bond_d 0.0041288958466 f_plane_restr 0.00287213634242
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1352 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 72
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing