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4-Chlorobenzoyl-CoA Ligase/Synthetase, I303G mutation, bound to 3,4-Dichlorobenzoate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T5D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 277 14-22% pentaerythritol propoxylate 426, 50 mM BTP, 1 mM ATP, 1 mM 3,4-DCB, pH 6.5-6.75, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.1 60.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.813 α = 90 b = 127.813 β = 90 c = 71.421 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 113 CCD ADSC QUANTUM 210 2005-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F2 0.97930 CHESS F2
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 2.76 30 99.5 0.088 11.5 5.2 17323
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 2.76 2.83 0.525 1.8
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 1T5D 2.76 30 16440 872 99.87 0.19455 0.19136 0.1894 0.25651 0.2546 RANDOM 57.054
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] 0.47 0.23 0.47 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.099 r_dihedral_angle_4_deg 20.782 r_dihedral_angle_3_deg 20.472 r_dihedral_angle_1_deg 7.375 r_scangle_it 4.457 r_mcangle_it 4.028 r_scbond_it 3.003 r_mcbond_it 2.649 r_angle_refined_deg 1.692 r_symmetry_vdw_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.099 r_dihedral_angle_4_deg 20.782 r_dihedral_angle_3_deg 20.472 r_dihedral_angle_1_deg 7.375 r_scangle_it 4.457 r_mcangle_it 4.028 r_scbond_it 3.003 r_mcbond_it 2.649 r_angle_refined_deg 1.692 r_symmetry_vdw_refined 0.323 r_nbtor_refined 0.322 r_nbd_refined 0.242 r_symmetry_hbond_refined 0.226 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.114 r_bond_refined_d 0.016 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3716 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection SCALEPACK data scaling MOLREP phasing