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Cyanide-bound structure of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase from Moorella thermoacetica, cyanide-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 2.74 55.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.83 α = 101.23 b = 136.768 β = 109.18 c = 141.611 γ = 103.87
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 ADSC QUANTUM 315 2002-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0000 ALS 5.0.2
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 2.15 50 96.3 0.051 25.911 3.5 346767
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 2.15 2.23 86.6 0.167 6.8 3.5
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 48.39 327121 17112 96.54 0.17432 0.17189 0.1718 0.22072 0.2189 RANDOM 35.631
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] -0.95 0.21 -0.52 0.42 -0.86 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.105 r_dihedral_angle_4_deg 21.56 r_dihedral_angle_3_deg 16.913 r_dihedral_angle_1_deg 6.597 r_scangle_it 4.122 r_scbond_it 2.63 r_angle_refined_deg 1.65 r_mcangle_it 1.549 r_mcbond_it 0.879 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.105 r_dihedral_angle_4_deg 21.56 r_dihedral_angle_3_deg 16.913 r_dihedral_angle_1_deg 6.597 r_scangle_it 4.122 r_scbond_it 2.63 r_angle_refined_deg 1.65 r_mcangle_it 1.549 r_mcbond_it 0.879 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.229 r_nbd_refined 0.211 r_symmetry_hbond_refined 0.18 r_xyhbond_nbd_refined 0.163 r_metal_ion_refined 0.146 r_chiral_restr 0.121 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 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 43318 Nucleic Acid Atoms Solvent Atoms 2155 Heterogen Atoms 172
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction