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Crystal structure of a benzoate coenzyme A ligase with 2-Thiophene Carboxylic 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 pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.26 45.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.644 α = 90 b = 94.609 β = 104.92 c = 95.701 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 1.72 39.58 97.57 0.097 0.079 21.84 4.4 99134 25.4
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 1.72 1.76 80 0.472 0.417 1.97 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1.72 39.58 541417 99134 5270 97.57 0.1584 0.15654 0.1683 0.19366 0.2042 RANDOM 25.67
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 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.618 r_dihedral_angle_4_deg 17.771 r_dihedral_angle_3_deg 12.73 r_dihedral_angle_1_deg 6.25 r_long_range_B_refined 5.627 r_long_range_B_other 5.564 r_scangle_other 4.491 r_scbond_other 3.082 r_scbond_it 3.08 r_mcangle_it 2.957
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.618 r_dihedral_angle_4_deg 17.771 r_dihedral_angle_3_deg 12.73 r_dihedral_angle_1_deg 6.25 r_long_range_B_refined 5.627 r_long_range_B_other 5.564 r_scangle_other 4.491 r_scbond_other 3.082 r_scbond_it 3.08 r_mcangle_it 2.957 r_mcangle_other 2.957 r_mcbond_it 2.167 r_mcbond_other 2.166 r_angle_refined_deg 1.974 r_angle_other_deg 1.01 r_chiral_restr 0.183 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7880 Nucleic Acid Atoms Solvent Atoms 572 Heterogen Atoms 74
Software Software Software Name Purpose HKL-2000 data collection Mol model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling Mol phasing