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HRAS G13D bound to GDP (H13GDP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6E6P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291.15 5.9% stabilization buffer (20 mM HEPES, 50 mM NaCl, 20 mM MgCl2, pH 7.5)
188.2 mM Calcium Acetate
18.8% PEG 3350
Crystals were grown in 2uL by 2uL drops of mother liquor to protein (7.7mg/mL)
Cryoprotectant for crystal diffraction: 70% mother liquor and 30% glycerol
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.571 α = 90 b = 71.41 β = 90 c = 94.861 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 IMAGE PLATE RIGAKU RAXIS IV++ 2014-11-25 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 1.95 50 82 0.092 0.1 0.037 8.1 6.5 175532 25256
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 1.95 1.98 47.3 0.596 0.695 0.345 0.689 3.2
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 6E6P 1.95 35.7 25252 2000 87.5 0.163 0.1688 0.218 0.2198 25.6642
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 3668 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 104
Software Software Software Name Purpose PHENIX refinement HKL-3000 data scaling PDB_EXTRACT data extraction HKL-3000 data reduction PHENIX phasing