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HRAS G13D bound to GppNHp (H13GNP)
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 7.5 291.15 128 mM Calcium acetate, 20.8% PEG 3350, 20% stabilization buffer (20 mM HEPES, 50 mM NaCl, 20 mM MgCl2, at pH 7.5), Crystals were grown in 2uL by 2 uL drops of mother liquor to protein (22 mg/mL), Cryoprotectant: 70% glycerol and 30% mother liquor
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.6 α = 90 b = 47.753 β = 118.31 c = 57.037 γ = 90
Symmetry Space Group C 1 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 173.15 IMAGE PLATE RIGAKU RAXIS IV++ 2014-03-28 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 1.9 30 95 0.088 0.104 0.054 6.8 3.5 33830 9755
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 1.9 1.93 84.4 0.542 0.67 0.388 0.668 2.5
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3K8Y 1.9 25.1 9751 974 94.89 0.168 0.23 0.213 27.7368
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 1285 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 34
Software Software Software Name Purpose HKL-2000 data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-3000 data reduction PHENIX phasing