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Crystal structure of NRas-G12D in complex with GDP and compound 13
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZIO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 0.1M Sodium Citrate pH5.5, 0.1M MgCl2, 16-22% Peg 4000
Crystal Properties Matthews coefficient Solvent content 2.04 39.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.016 α = 90 b = 46.237 β = 89.19 c = 79.61 γ = 90
Symmetry Space Group P 1 21 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 9M 2023-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.92011 NSLS-II 17-ID-1
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 1.56 29.39 99.83 0.998 8.58 3.6 58131
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 1.56 1.59 99.54 0.313
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 1.56 29.39 1.36 44933 2218 99.68 0.1754 0.1736 0.1725 0.2093 0.2074
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 21.363 f_angle_d 1.247 f_chiral_restr 0.067 f_plane_restr 0.01 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2700 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 144
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PDB_EXTRACT data extraction PHASER phasing