☰ Navigation Tabs
BurG (holo) in complex with gonyenediol (14), trigonic acid (6) and DMS: 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 8 293 0.1 M Inidazole; 10% PEG 8K, 2 mM NAD+, 5 mM MgCl2, 2 mM gonydiol (5)
Crystal Properties Matthews coefficient Solvent content 2.1 41.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.88 α = 90 b = 76.13 β = 105.14 c = 79.11 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 2021-01-31 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 1.6 30 98.2 0.091 7.3 3.1 82909
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 1.6 1.7 0.573 1.9
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 1.6 30 78752 4145 98.27 0.135 0.1337 0.136 0.1594 0.161 RANDOM 17.986
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] 0.68 -0.55 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.011 r_dihedral_angle_4_deg 19.017 r_dihedral_angle_3_deg 12.128 r_dihedral_angle_1_deg 6.04 r_rigid_bond_restr 1.589 r_angle_refined_deg 1.442 r_angle_other_deg 1.417 r_chiral_restr 0.075 r_bond_refined_d 0.006 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.011 r_dihedral_angle_4_deg 19.017 r_dihedral_angle_3_deg 12.128 r_dihedral_angle_1_deg 6.04 r_rigid_bond_restr 1.589 r_angle_refined_deg 1.442 r_angle_other_deg 1.417 r_chiral_restr 0.075 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5225 Nucleic Acid Atoms Solvent Atoms 473 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing