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BurG (holo) in complex with cyclopropane-1,1-dicarboxylate (7): 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; 20% PEG 10K, 2 mM NAD+, 5 mM MgCl2. 2mM (7)
Crystal Properties Matthews coefficient Solvent content 2.06 40.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.63 α = 90 b = 83.26 β = 90 c = 101.21 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 PIXEL DECTRIS EIGER2 X 16M 2020-09-12 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 1.9 30 97.7 0.085 10.2 4.2 49898
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 1.9 2 99.5 0.571 2.1
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 1.9 30 47391 2494 97.71 0.1974 0.1952 0.2044 0.2282 0.2398 RANDOM 27.451
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] -0.03 -0.66 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.426 r_dihedral_angle_4_deg 16.613 r_dihedral_angle_3_deg 13.415 r_dihedral_angle_1_deg 5.879 r_angle_refined_deg 1.198 r_angle_other_deg 1.17 r_rigid_bond_restr 0.399 r_chiral_restr 0.049 r_bond_refined_d 0.004 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.426 r_dihedral_angle_4_deg 16.613 r_dihedral_angle_3_deg 13.415 r_dihedral_angle_1_deg 5.879 r_angle_refined_deg 1.198 r_angle_other_deg 1.17 r_rigid_bond_restr 0.399 r_chiral_restr 0.049 r_bond_refined_d 0.004 r_bond_other_d 0.003 r_gen_planes_refined 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5221 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing