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Crystal structure of a benzoate coenzyme A ligase with 2-Fluoro benzoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V7B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 15 % PEG 3350, 0.1 M Tris pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.31 46.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.885 α = 90 b = 95.749 β = 110.43 c = 98.605 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 CCD MARMOSAIC 300 mm CCD 2011-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97872 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.77 50 97.8 0.105 0.083 12.68 3.5 92681
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.81 80.81 0.475 0.437 1.55 2
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 2V7B 1.77 41.61 92653 4931 97.82 0.16127 0.15913 0.1711 0.20167 0.2139 RANDOM 19.3
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.708 r_dihedral_angle_4_deg 18.49 r_dihedral_angle_3_deg 13.037 r_dihedral_angle_1_deg 6.596 r_long_range_B_refined 5.232 r_long_range_B_other 5.063 r_scangle_other 3.875 r_mcangle_it 2.673 r_scbond_it 2.611 r_scbond_other 2.569
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.708 r_dihedral_angle_4_deg 18.49 r_dihedral_angle_3_deg 13.037 r_dihedral_angle_1_deg 6.596 r_long_range_B_refined 5.232 r_long_range_B_other 5.063 r_scangle_other 3.875 r_mcangle_it 2.673 r_scbond_it 2.611 r_scbond_other 2.569 r_mcangle_other 2.37 r_angle_refined_deg 1.961 r_mcbond_it 1.877 r_mcbond_other 1.876 r_angle_other_deg 0.943 r_chiral_restr 0.128 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 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 7851 Nucleic Acid Atoms Solvent Atoms 738 Heterogen Atoms 30
Software Software Software Name Purpose HKL-2000 data collection mol model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling mol phasing