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Crystal structure of a benzoate coenzyme A ligase with p-Toluic acid and o-Toluic 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 2.3 46.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.716 α = 90 b = 95.366 β = 104.69 c = 95.785 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 1.73 50 95.7 0.09 0.06 17.8 4.8 96640 22.18
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 1.73 1.76 72.1 0.654 0.574 1.52 3.1
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 2V7B 1.73 32.23 96612 5121 95.69 0.16121 0.1594 0.1719 0.19525 0.2028 RANDOM 22.318
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.094 r_dihedral_angle_4_deg 18.174 r_dihedral_angle_3_deg 12.403 r_dihedral_angle_1_deg 6.601 r_long_range_B_refined 5.641 r_long_range_B_other 5.562 r_scangle_other 4.351 r_scbond_it 2.96 r_scbond_other 2.96 r_mcangle_it 2.778
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.094 r_dihedral_angle_4_deg 18.174 r_dihedral_angle_3_deg 12.403 r_dihedral_angle_1_deg 6.601 r_long_range_B_refined 5.641 r_long_range_B_other 5.562 r_scangle_other 4.351 r_scbond_it 2.96 r_scbond_other 2.96 r_mcangle_it 2.778 r_mcangle_other 2.778 r_mcbond_it 2.056 r_mcbond_other 2.051 r_angle_refined_deg 1.966 r_angle_other_deg 0.952 r_chiral_restr 0.158 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7792 Nucleic Acid Atoms Solvent Atoms 544 Heterogen Atoms 88
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling