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Crystal structure of the E190A mutant of o-succinylbenzoate synthase from Escherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FHU PDB entry 1FHU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.8 298 0.1 M MES, 75 mM Sodium molybdate, 25% (v/v) PEG 4000, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.1 41.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.475 α = 90 b = 77.388 β = 90.08 c = 110.677 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 315 Vertical focusing mirror 2006-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.979462 SSRL BL9-1
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 43.291 96.5 0.131 0.131 4.5 3.7 76466 1
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 2 2.05 82.8 0.018 1.832 0.3 3.4 4815
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 1FHU 2.3 43.291 48414 48414 2598 97.46 0.225 0.225 0.222 0.2247 0.29 0.2906 RANDOM 34.243
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] 4.49 1.18 -1.79 -2.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.76 r_dihedral_angle_4_deg 18.98 r_dihedral_angle_3_deg 18.124 r_dihedral_angle_1_deg 7.801 r_scangle_it 1.796 r_scbond_it 1.301 r_angle_refined_deg 1.278 r_angle_other_deg 0.889 r_mcbond_it 0.766 r_mcangle_it 0.761
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.76 r_dihedral_angle_4_deg 18.98 r_dihedral_angle_3_deg 18.124 r_dihedral_angle_1_deg 7.801 r_scangle_it 1.796 r_scbond_it 1.301 r_angle_refined_deg 1.278 r_angle_other_deg 0.889 r_mcbond_it 0.766 r_mcangle_it 0.761 r_symmetry_vdw_refined 0.339 r_symmetry_vdw_other 0.234 r_nbd_refined 0.217 r_nbd_other 0.207 r_symmetry_hbond_refined 0.175 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.16 r_mcbond_other 0.093 r_nbtor_other 0.085 r_bond_refined_d 0.01 r_bond_other_d 0.007 r_gen_planes_refined 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9325 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection MOSFLM data reduction