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Native structure of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase from Moorella thermoacetica, water-bound C-cluster.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MJG PDB entry 1MJG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 298 8% PEG MME 5000, 20% glycerol, 200 mM calcium acetate, 100 mM Pipes, pH 6.5, 2 mM dithiothreitol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.71 54.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.651 α = 101.26 b = 136.87 β = 109.11 c = 140.864 γ = 104.08
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 MARMOSAIC 325 mm CCD 2003-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.95469 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.15 36.96 92.3 0.067 2.1 310437 326694
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.21 90.4 0.46 2.3 2.1
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 Rigid body refinement from previously solved structure THROUGHOUT PDB entry 1MJG 2.15 36.96 310437 16243 92.3 0.18902 0.18627 0.1873 0.24154 0.2397 RANDOM 36.935
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] -1.09 0.15 -0.47 0.2 -1.27 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.533 r_dihedral_angle_4_deg 21.299 r_dihedral_angle_3_deg 18.396 r_dihedral_angle_1_deg 7.141 r_scangle_it 4.248 r_scbond_it 2.818 r_angle_refined_deg 1.871 r_mcangle_it 1.648 r_mcbond_it 0.954 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.533 r_dihedral_angle_4_deg 21.299 r_dihedral_angle_3_deg 18.396 r_dihedral_angle_1_deg 7.141 r_scangle_it 4.248 r_scbond_it 2.818 r_angle_refined_deg 1.871 r_mcangle_it 1.648 r_mcbond_it 0.954 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.25 r_nbd_refined 0.228 r_symmetry_hbond_refined 0.179 r_xyhbond_nbd_refined 0.172 r_metal_ion_refined 0.151 r_chiral_restr 0.134 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 43306 Nucleic Acid Atoms Solvent Atoms 1413 Heterogen Atoms 164
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling