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Crystal structure of H-Ras G12V in complex with GppNHp (state 1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EFL PDB ENTRY 4EFL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1M MES, 0.2M ammonium sulfate, 30% (w/v) PEG 5000 MME, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.23 44.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.638 α = 90 b = 81.833 β = 90 c = 121.761 γ = 90
Symmetry Space Group I 2 2 2
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 RAYONIX MX225HE mirrors 2010-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 33.32 99.9 0.097 0.097 5.4 7.2 14109 14109
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 100 0.3 0.3 2.4 7.3 2037
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4EFL 1.9 33.32 13401 13401 704 99.87 0.18769 0.18769 0.18587 0.1867 0.22111 0.2221 RANDOM 19.132
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 r_dihedral_angle_2_deg 35.475 r_dihedral_angle_3_deg 14.104 r_dihedral_angle_4_deg 11.781 r_dihedral_angle_1_deg 5.151 r_scangle_it 3.779 r_scbond_it 2.168 r_mcangle_it 1.354 r_angle_refined_deg 1.211 r_mcbond_it 0.678 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.475 r_dihedral_angle_3_deg 14.104 r_dihedral_angle_4_deg 11.781 r_dihedral_angle_1_deg 5.151 r_scangle_it 3.779 r_scbond_it 2.168 r_mcangle_it 1.354 r_angle_refined_deg 1.211 r_mcbond_it 0.678 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1326 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 33
Software Software Software Name Purpose BSS data collection REFMAC refinement MOSFLM data reduction SCALA data scaling