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BurG (holo) in complex with (Z)-2,3-dihydroxy-6-methyl-hept-2-enoate (13): 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; 0.8 M LiCl, 8% PEG 4K, 2 mM NAD+, 5 mM MgCl2, 2 mM 13
Crystal Properties Matthews coefficient Solvent content 2.06 40.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.81 α = 90 b = 83.61 β = 90 c = 100.73 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 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 2.05 30 98.5 0.112 7.4 4.4 40243
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 2.05 2.15 0.596 2.4
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 2.05 30 38214 2012 98.48 0.2053 0.2034 0.2179 0.239 0.2561 RANDOM 28.561
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] -0.84 -1.87 2.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.418 r_dihedral_angle_4_deg 16.766 r_dihedral_angle_3_deg 13.56 r_dihedral_angle_1_deg 6.363 r_angle_refined_deg 1.293 r_angle_other_deg 1.173 r_rigid_bond_restr 0.67 r_chiral_restr 0.052 r_gen_planes_refined 0.004 r_bond_refined_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.418 r_dihedral_angle_4_deg 16.766 r_dihedral_angle_3_deg 13.56 r_dihedral_angle_1_deg 6.363 r_angle_refined_deg 1.293 r_angle_other_deg 1.173 r_rigid_bond_restr 0.67 r_chiral_restr 0.052 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 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 111 Heterogen Atoms 117
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing