☰ Navigation Tabs
The structure of Microcin C7 biosynthetic enzyme MccB in complex with N-formylated MccA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H9G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 282 0.1 M Magnesium formate, 15% w/v Polyethylene glycol 3350, and 6% w/v 1,6-Hexanediol
Crystal Properties Matthews coefficient Solvent content 1.73 29.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.094 α = 90 b = 76.059 β = 90 c = 131.902 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 80 CCD RAYONIX MX-300 2018-01-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.078 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 65.98 96.1 14.2 14 59837
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.725
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 3H9G 1.7 65.98 56811 2991 96.09 0.15692 0.1547 0.1648 0.19868 0.2062 RANDOM 20.757
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] 0.9 0.57 -1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.475 r_dihedral_angle_4_deg 21.547 r_dihedral_angle_3_deg 15.16 r_dihedral_angle_1_deg 6.75 r_long_range_B_refined 5.216 r_long_range_B_other 5.216 r_scangle_other 4.339 r_scbond_it 2.876 r_scbond_other 2.875 r_mcangle_other 2.584
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.475 r_dihedral_angle_4_deg 21.547 r_dihedral_angle_3_deg 15.16 r_dihedral_angle_1_deg 6.75 r_long_range_B_refined 5.216 r_long_range_B_other 5.216 r_scangle_other 4.339 r_scbond_it 2.876 r_scbond_other 2.875 r_mcangle_other 2.584 r_mcangle_it 2.582 r_mcbond_it 1.748 r_mcbond_other 1.747 r_angle_refined_deg 1.7 r_angle_other_deg 1.07 r_chiral_restr 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5564 Nucleic Acid Atoms Solvent Atoms 439 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data scaling PHENIX model building BUCCANEER model building PHENIX phasing XDS data reduction