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Crystal Structure of Q61L H-Ras-GppNHp bound to the RBD of Raf Kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K8Y PDB 3K8Y for Chain A and PDB 1GUA for Chain B experimental model PDB 1GUA PDB 3K8Y for Chain A and PDB 1GUA for Chain B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 291 Protein solution: 10 - 18 mg/mL, 50 mM HEPES, pH 7.2, 50 mM NaCl, 10mM MgCl2 5% Glycerol, 1mM DTE, 10 M ZnCl2 Reservoir solution:200mM calcium acetate, 100mM sodium cacodylate pH 6.5, 18% PEG 8000. Drop: 3uL protein, 3uL reservoir , VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 4.06 69.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.4 α = 90 b = 91.4 β = 90 c = 93.11 γ = 120
Symmetry Space Group P 3 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 100 CCD MARMOSAIC 300 mm CCD crystal 2011-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.25 32.6 0.18 4.6 6462 6462 3 3
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB 3K8Y for Chain A and PDB 1GUA for Chain B 3.25 32.6 6339 668 85.6 0.2754 0.2505 0.271 0.2255
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] 0.0605 0.0605 -0.1211
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.773 f_angle_d 0.597 f_chiral_restr 0.041 f_bond_d 0.009 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1860 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 33
Software Software Software Name Purpose MAR345 data collection SERGUI data collection PHENIX model building PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing