☰ Navigation Tabs
BurG E232Q mutant (holo) in complex with enol-oxalacetate (15): Biosynthesis of cyclopropanol rings in bacterial toxins
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7PCC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1 M Tris; o.2 M NaAc, 16% PEG 4K, 2 mM NAD+, 5 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.15 42.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.29 α = 90 b = 76.03 β = 106.14 c = 78.23 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 PIXEL DECTRIS EIGER X 16M 2021-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 1.35 30 97.3 0.068 8.1 3 139870
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 1.35 1.45 0.536
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 7PCC 1.35 30 132865 6993 97.39 0.1573 0.1561 0.1583 0.1795 0.1824 RANDOM 13.772
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] 1.08 -0.88 -0.92 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.029 r_dihedral_angle_4_deg 17.31 r_dihedral_angle_3_deg 11.252 r_dihedral_angle_1_deg 5.962 r_angle_other_deg 1.477 r_angle_refined_deg 1.437 r_rigid_bond_restr 0.996 r_chiral_restr 0.071 r_gen_planes_refined 0.007 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.029 r_dihedral_angle_4_deg 17.31 r_dihedral_angle_3_deg 11.252 r_dihedral_angle_1_deg 5.962 r_angle_other_deg 1.477 r_angle_refined_deg 1.437 r_rigid_bond_restr 0.996 r_chiral_restr 0.071 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5209 Nucleic Acid Atoms Solvent Atoms 749 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing