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The Structure of the Ternary Complex of Carboxymethyl Coenzyme A and Oxalateacetate with Citrate Synthase from the Thermophilic Archaeonthermoplasma Acidophilum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O7X 1O7X_A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 280 15-18% Peg 400, 100mM Hepes 7-8.5, 200 mM Sodium Acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 280K
Crystal Properties Matthews coefficient Solvent content 2.29 46.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.705 α = 99.34 b = 74.221 β = 98.34 c = 89.874 γ = 114.38
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 NOIR-1 DOUBLE CRYSTAL 2006-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.0000 ALS 4.2.2
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 2.4 43.09 97.5 0.101 6.1 3.17 59729 58219
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 (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1O7X_A 2.5 43.09 51542 2604 97.52 0.203 0.203 0.2 0.1989 0.261 RANDOM 37.683
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] -1.23 -3.99 -1.25 -1.48 1.25 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.822 r_dihedral_angle_3_deg 15.404 r_dihedral_angle_4_deg 12.564 r_dihedral_angle_1_deg 4.626 r_angle_refined_deg 0.981 r_scangle_it 0.83 r_mcangle_it 0.484 r_scbond_it 0.479 r_nbtor_refined 0.295 r_mcbond_it 0.268
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.822 r_dihedral_angle_3_deg 15.404 r_dihedral_angle_4_deg 12.564 r_dihedral_angle_1_deg 4.626 r_angle_refined_deg 0.981 r_scangle_it 0.83 r_mcangle_it 0.484 r_scbond_it 0.479 r_nbtor_refined 0.295 r_mcbond_it 0.268 r_nbd_refined 0.175 r_symmetry_vdw_refined 0.142 r_symmetry_hbond_refined 0.111 r_xyhbond_nbd_refined 0.108 r_chiral_restr 0.069 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11965 Nucleic Acid Atoms Solvent Atoms 959 Heterogen Atoms 244
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction d*TREK data reduction d*TREK data scaling CNS phasing