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KRAS G13D bound to GDP (K13GDP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K8Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 291.15 27.5% PEG 3350, 125 mM Na(OAc), 122 mM sodium citrate, 4.0% stabilization buffer (20 mM HEPES, 50 mM NaCl, 20 mM MgCl2, at pH 7.5), Crystals grown in 1uL by 1uL drops of mother liquor to protein (18 mg/mL), No cryoprotectant used for diffraction
Crystal Properties Matthews coefficient Solvent content 1.81 31.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.096 α = 90 b = 37.829 β = 90 c = 100.171 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 173.15 IMAGE PLATE RIGAKU RAXIS IV++ 2014-08-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.93 50 99 0.101 0.111 0.044 6.4 5.9 63590 10737
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 1.93 1.96 87.9 0.394 0.463 0.235 0.796 3.1
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3K8Y 1.93 34 10733 1068 98.99 0.165 0.1687 0.225 0.2278 22.9541
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1302 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 30
Software Software Software Name Purpose HKL-2000 data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-3000 data reduction PHENIX phasing