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tryptophanyl-tRNA synthetase Val144Pro mutant from B. subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FIO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 0.05 M MgCl2, 0.05 M HEPES/NaOH pH 7, 25% PEG550, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.14 42.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.258 α = 90 b = 119.816 β = 90 c = 127.353 γ = 90
Symmetry Space Group P 21 21 21
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 TOROIDAL MIRROR 2010-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9805 Diamond I04
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 2.8 30 99.9 0.05 0.05 13.5 7.1 19307 19307 71.8
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) 2.8 2.95 100 0.3 0.3 2.6 7.3 2763
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 3FIO 2.8 29.95 19260 19260 913 99.97 0.23714 0.23714 0.2352 0.2348 0.27504 0.2688 RANDOM 45.543
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] -3.04 3.73 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.948 r_dihedral_angle_4_deg 16.944 r_dihedral_angle_3_deg 16.829 r_dihedral_angle_1_deg 5.989 r_scangle_it 2.03 r_scbond_it 1.324 r_angle_refined_deg 1.314 r_mcangle_it 1.118 r_mcbond_it 1.03 r_angle_other_deg 0.864
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.948 r_dihedral_angle_4_deg 16.944 r_dihedral_angle_3_deg 16.829 r_dihedral_angle_1_deg 5.989 r_scangle_it 2.03 r_scbond_it 1.324 r_angle_refined_deg 1.314 r_mcangle_it 1.118 r_mcbond_it 1.03 r_angle_other_deg 0.864 r_symmetry_vdw_other 0.319 r_nbd_refined 0.233 r_nbd_other 0.196 r_symmetry_hbond_refined 0.189 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.174 r_symmetry_vdw_refined 0.155 r_xyhbond_nbd_other 0.142 r_mcbond_other 0.108 r_nbtor_other 0.089 r_chiral_restr 0.068 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4934 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling