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Crystal structure of H-Ras WT in complex with GppNHp (state 1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KKN PDB ENTRY 3KKN
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 2.24 45.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.666 α = 90 b = 81.783 β = 90 c = 121.726 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 2009-10-07 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 36.35 99.2 0.073 0.073 7.8 7.3 13986 13986
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 98.6 0.302 0.302 2.4 7.4 2004
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3KKN 1.9 36.35 13287 13287 699 99.03 0.18524 0.18524 0.1842 0.20433 0.2011 RANDOM 18.132
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.982 r_dihedral_angle_3_deg 13.529 r_dihedral_angle_4_deg 13.362 r_dihedral_angle_1_deg 5.156 r_scangle_it 3.665 r_scbond_it 2.11 r_mcangle_it 1.334 r_angle_refined_deg 1.169 r_mcbond_it 0.669 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.982 r_dihedral_angle_3_deg 13.529 r_dihedral_angle_4_deg 13.362 r_dihedral_angle_1_deg 5.156 r_scangle_it 3.665 r_scbond_it 2.11 r_mcangle_it 1.334 r_angle_refined_deg 1.169 r_mcbond_it 0.669 r_chiral_restr 0.072 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1323 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 33
Software Software Software Name Purpose BSS data collection REFMAC refinement MOSFLM data reduction SCALA data scaling