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Crystal structure analysis of a fluorescent form of H-Ras p21 in complex with R-caged GTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5P21 pdb entry 5p21
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 291.15 protein solution: 64 mM TRIS pH 7.6, 20 mM magnesium chloride, 10 mM DTT, 0,1 mM sodium azide;
reservoir solution: 100 mM HEPES pH 7.2, 200 mM magnesium acetate, 16% PEG 8000 (freshly prepared)
mixture of equal volumes of protein and reservoir solution, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
Crystal Properties Matthews coefficient Solvent content 2.27 45.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.3 α = 90 b = 69.3 β = 90 c = 35.51 γ = 90
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 ADSC QUANTUM 4 mirrors 2004-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.939 ESRF ID14-4
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 69.34 99.9 0.052 0.052 13.82 5.9 536019 78838 -3 -3 14
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 1.05 99.9 0.679 0.679 2.43 4 12300
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 5p21 1.05 69.34 78796 78796 3909 99.93 0.157 0.157 0.156 0.2088 0.181 0.2359 RANDOM 6.21
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] -0.68 -0.68 1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.73 r_dihedral_angle_4_deg 19.607 r_dihedral_angle_3_deg 14.091 r_dihedral_angle_1_deg 6.228 r_scangle_it 2.845 r_scbond_it 2.209 r_angle_refined_deg 1.855 r_mcangle_it 1.287 r_mcbond_it 1.183 r_angle_other_deg 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.73 r_dihedral_angle_4_deg 19.607 r_dihedral_angle_3_deg 14.091 r_dihedral_angle_1_deg 6.228 r_scangle_it 2.845 r_scbond_it 2.209 r_angle_refined_deg 1.855 r_mcangle_it 1.287 r_mcbond_it 1.183 r_angle_other_deg 0.86 r_symmetry_vdw_other 0.285 r_symmetry_hbond_refined 0.27 r_xyhbond_nbd_refined 0.255 r_nbd_refined 0.24 r_mcbond_other 0.235 r_symmetry_vdw_refined 0.195 r_nbd_other 0.193 r_nbtor_refined 0.191 r_symmetry_hbond_other 0.11 r_chiral_restr 0.095 r_nbtor_other 0.09 r_metal_ion_refined 0.02 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1317 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 65
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction ProDC data collection MOLREP phasing