☰ Navigation Tabs
Crystal structure of the K133R mutant of o-Succinylbenzoate synthase (OSBS) from Escherichia coli. Complex with SHCHC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FHV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5.5 293 The K133R mutant of OSBS was concentrated to 15 mg/ml, dialyzed
against 5 mM Tris pH 8.3 containing 2 mM MgCl2, drop frozen as small
pellets in liquid nitrogen and stored at -80 C. Crystals were grown
at 20 C by small-scale batch experiments by combining 15 ml of protein
solution and 15 ml of a solution containing 12-13% MePEG 5000, 100 mM
sodium acetate, 60 mM MgCl2, at pH 5.5. SHCHC was included in the
crystallization at a final concentration of approximately 2.5 mM., microbatch, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.2 α = 90 b = 82.9 β = 90 c = 56.2 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 150 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-D 0.9790 APS 14-BM-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.62 31 99.9 0.046 41 7.1 43694 43694 25.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.62 1.68 98.9 0.293 17.1
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 1fhv 1.62 30 41456 41456 2190 99.82 0.16911 0.1691 0.16743 0.1809 0.20024 0.2135 RANDOM 17.89
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] -0.58 -1.38 1.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.573 r_scangle_it 4.732 r_scbond_it 3.057 r_mcangle_it 2.162 r_angle_refined_deg 1.615 r_angle_other_deg 1.237 r_mcbond_it 1.236 r_symmetry_vdw_refined 0.31 r_symmetry_vdw_other 0.287 r_nbd_other 0.253
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.573 r_scangle_it 4.732 r_scbond_it 3.057 r_mcangle_it 2.162 r_angle_refined_deg 1.615 r_angle_other_deg 1.237 r_mcbond_it 1.236 r_symmetry_vdw_refined 0.31 r_symmetry_vdw_other 0.287 r_nbd_other 0.253 r_nbd_refined 0.247 r_xyhbond_nbd_refined 0.161 r_symmetry_hbond_refined 0.155 r_chiral_restr 0.094 r_nbtor_other 0.087 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_gen_planes_other 0.008 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2488 Nucleic Acid Atoms Solvent Atoms 344 Heterogen Atoms 18
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling MOLREP phasing REFMAC refinement HKL-2000 data reduction