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Acetyl-CoA Synthetase, wild-type with acetate, AMP, and CoA bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PG4 pdb entry 1PG4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 287 6-15% PEG 8000, 9-13% ethylene glycol, 50 mM BTP, 1 mM CoA, 1 mM Acetate, 1 mM AMP, 1 mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Properties Matthews coefficient Solvent content 2.42 49.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.906 α = 90 b = 94.933 β = 90 c = 161.814 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 CUSTOM-MADE 2003-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C 0.95 NSLS X12C
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 2.58 81.65 98.9 0.072 10.8 5.1 42079 38.3
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 2.58 2.7 100 0.224 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 FOURIER SYNTHESIS THROUGHOUT pdb entry 1PG4 2.58 81.65 42079 2261 98.97 0.186 0.183 0.185 0.247 0.2469 RANDOM 18.048
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] 0.71 -1.14 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.148 r_dihedral_angle_4_deg 20.21 r_dihedral_angle_3_deg 15.837 r_dihedral_angle_1_deg 6.416 r_scangle_it 2.681 r_scbond_it 1.672 r_angle_refined_deg 1.532 r_mcangle_it 1.019 r_mcbond_it 0.611 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.148 r_dihedral_angle_4_deg 20.21 r_dihedral_angle_3_deg 15.837 r_dihedral_angle_1_deg 6.416 r_scangle_it 2.681 r_scbond_it 1.672 r_angle_refined_deg 1.532 r_mcangle_it 1.019 r_mcbond_it 0.611 r_nbtor_refined 0.31 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.179 r_symmetry_hbond_refined 0.148 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9828 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 150
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SCALEPACK data scaling REFMAC phasing