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4-Chlorobenzoyl-CoA Ligase/Synthetase in the Thioester-forming Conformation, bound to 4-chlorophenacyl-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T5D 1T5D, residues 1-402
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 14-18% PEG 1000, 75 mM Magnesium Nitrate, 100 mM MOPS, 1 mM AMP, 1 mM 4-Chlorophenacyl-CoA, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.27 45.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.507 α = 90 b = 87.789 β = 90 c = 186.06 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 113 CCD ADSC QUANTUM 315 2006-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.979469 SSRL BL9-1
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 35 94.6 0.086 30.9 5.6 64355 60959 18.9
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 2.05 74.3 0.174 6.7 3442
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 (All) 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, residues 1-402 2 35 64355 60959 3258 94.65 0.16798 0.16798 0.16576 0.1676 0.20912 0.2108 RANDOM 18.886
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] 1.36 -1.54 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.571 r_dihedral_angle_4_deg 17.111 r_dihedral_angle_3_deg 13.126 r_dihedral_angle_1_deg 5.64 r_scangle_it 2.176 r_scbond_it 1.323 r_angle_refined_deg 1.234 r_mcangle_it 0.759 r_mcbond_it 0.454 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.571 r_dihedral_angle_4_deg 17.111 r_dihedral_angle_3_deg 13.126 r_dihedral_angle_1_deg 5.64 r_scangle_it 2.176 r_scbond_it 1.323 r_angle_refined_deg 1.234 r_mcangle_it 0.759 r_mcbond_it 0.454 r_nbtor_refined 0.297 r_nbd_refined 0.183 r_symmetry_vdw_refined 0.162 r_symmetry_hbond_refined 0.145 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7604 Nucleic Acid Atoms Solvent Atoms 800 Heterogen Atoms 180
Software Software Software Name Purpose SSRL data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling