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Crystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase in complex with compound 7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W2X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 298 0.1 M Na citrate ,pH 5.5, 200 mM NaCl, 8% PEG8000, 10% glycerol, vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.18 70.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 246.716 α = 90 b = 121.678 β = 94.23 c = 145.991 γ = 90
Symmetry Space Group C 1 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 IMAGE PLATE RIGAKU RAXIS HTC 2006-01-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
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 2.43 40.7 98.3 0.065 21.112 3.5 159230
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) 2.43 2.52 91.9 0.614 3.4 14879
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 1W2X 2.43 40.7 159203 15829 98.48 0.166 0.16 0.1692 0.218 0.2189 RANDOM 56.371
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] -1.71 -0.24 2.86 -1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38 r_dihedral_angle_3_deg 19.642 r_dihedral_angle_4_deg 18.672 r_dihedral_angle_1_deg 7.798 r_scangle_it 3.718 r_scbond_it 2.475 r_angle_refined_deg 1.993 r_mcangle_it 1.938 r_mcbond_it 1.302 r_angle_other_deg 1.035
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38 r_dihedral_angle_3_deg 19.642 r_dihedral_angle_4_deg 18.672 r_dihedral_angle_1_deg 7.798 r_scangle_it 3.718 r_scbond_it 2.475 r_angle_refined_deg 1.993 r_mcangle_it 1.938 r_mcbond_it 1.302 r_angle_other_deg 1.035 r_symmetry_hbond_refined 0.361 r_xyhbond_nbd_refined 0.275 r_symmetry_vdw_other 0.254 r_mcbond_other 0.241 r_nbd_refined 0.232 r_nbd_other 0.21 r_nbtor_refined 0.188 r_xyhbond_nbd_other 0.18 r_symmetry_vdw_refined 0.167 r_chiral_restr 0.128 r_nbtor_other 0.096 r_bond_refined_d 0.024 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16257 Nucleic Acid Atoms Solvent Atoms 2403 Heterogen Atoms 110
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data scaling