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Crystal structure of the 6-carboxyhexanoate-CoA ligase (BioW)from Bacillus subtilis in complex with coenzyme A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FLG PDB ENTRY 5FLG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 19% PEG400, 0.1 M HEPES PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.8 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.59 α = 90 b = 78.36 β = 90 c = 166.43 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 PILATUS 2015-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 2.25 70.89 99.8 0.06 18.8 6.4 32279 2
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 2.25 2.37 99.7 0.76 2 5.1
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 PDB ENTRY 5FLG 2.25 57.11 30569 1647 99.74 0.21895 0.21705 0.2249 0.25175 0.2585 RANDOM 58.666
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] 9.36 -6.4 -2.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.206 r_dihedral_angle_4_deg 20.64 r_dihedral_angle_3_deg 15.573 r_dihedral_angle_1_deg 7.772 r_angle_refined_deg 1.329 r_angle_other_deg 0.784 r_chiral_restr 0.078 r_gen_planes_refined 0.014 r_bond_refined_d 0.012 r_gen_planes_other 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.206 r_dihedral_angle_4_deg 20.64 r_dihedral_angle_3_deg 15.573 r_dihedral_angle_1_deg 7.772 r_angle_refined_deg 1.329 r_angle_other_deg 0.784 r_chiral_restr 0.078 r_gen_planes_refined 0.014 r_bond_refined_d 0.012 r_gen_planes_other 0.006 r_bond_other_d 0.003 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3979 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data reduction xia2 data scaling XSCALE data scaling PHASER phasing