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The Structure of the Binary Complex of Oxalateacetate with Citrate Synthase from the Thermophilic Archaeon Thermolasma 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 8.5 280 17 % PEG 4000, 100mM Hepes 8.5, 200mM Sodium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 280K
Crystal Properties Matthews coefficient Solvent content 2.37 48.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.526 α = 90 b = 97.447 β = 93.1 c = 106.937 γ = 90
Symmetry Space Group P 1 21 1
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 1.7 41.38 96.8 0.09 10 6.19 170739 170738
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 1.7 1.76 94.5 0.48 2.9 6.03 16592
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 (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 1O7X_A 1.7 41.38 170707 170707 8560 96.77 0.183 0.181 0.1765 0.234 0.23 RANDOM 26.348
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] -0.17 -0.05 0.11 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.618 r_dihedral_angle_4_deg 15.864 r_dihedral_angle_3_deg 14.959 r_dihedral_angle_1_deg 5.562 r_scangle_it 3.921 r_scbond_it 2.619 r_angle_refined_deg 1.602 r_mcangle_it 1.563 r_mcbond_it 1.108 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.618 r_dihedral_angle_4_deg 15.864 r_dihedral_angle_3_deg 14.959 r_dihedral_angle_1_deg 5.562 r_scangle_it 3.921 r_scbond_it 2.619 r_angle_refined_deg 1.602 r_mcangle_it 1.563 r_mcbond_it 1.108 r_nbtor_refined 0.306 r_nbd_refined 0.211 r_symmetry_hbond_refined 0.187 r_symmetry_vdw_refined 0.182 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.121 r_bond_refined_d 0.02 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11958 Nucleic Acid Atoms Solvent Atoms 2228 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement CNS refinement d*TREK data scaling PDB_EXTRACT data extraction CNS phasing