☰ Navigation Tabs
NAD+-dependent fungal formate dehydrogenase from Chaetomium thermophilum: A complex with the reduced form of the cofactor NADH and the substrate formate at a secondary site.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 291 0.1 M Bis-Tris, pH 6.5, 20% w/v PEG 5000 MME, 2.5 mM NAD+
Crystal Properties Matthews coefficient Solvent content 2.45 49.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.568 α = 85.592 b = 94.756 β = 89.932 c = 94.604 γ = 81.614
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2018-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.26 47.06 87 0.999 7.6 1.7 407315 22.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.26 1.28 48.1 0.215 1.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5dna 1.26 46.774 407312 20297 86.99 0.17 0.1692 0.1693 0.1931 0.1931 23.935
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] 0.088 0.304 -0.244 0.444 -0.21 -0.484
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.662 r_dihedral_angle_4_deg 13.685 r_dihedral_angle_3_deg 12.879 r_lrange_it 7.896 r_lrange_other 7.896 r_scangle_it 6.923 r_scangle_other 6.923 r_dihedral_angle_1_deg 6.611 r_scbond_it 5.637 r_scbond_other 5.636
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.662 r_dihedral_angle_4_deg 13.685 r_dihedral_angle_3_deg 12.879 r_lrange_it 7.896 r_lrange_other 7.896 r_scangle_it 6.923 r_scangle_other 6.923 r_dihedral_angle_1_deg 6.611 r_scbond_it 5.637 r_scbond_other 5.636 r_mcangle_it 4.96 r_mcangle_other 4.956 r_mcbond_it 4.25 r_mcbond_other 4.25 r_angle_other_deg 2.297 r_angle_refined_deg 1.766 r_nbd_refined 0.215 r_symmetry_nbd_other 0.212 r_symmetry_xyhbond_nbd_refined 0.204 r_symmetry_nbd_refined 0.194 r_xyhbond_nbd_refined 0.177 r_nbd_other 0.173 r_nbtor_refined 0.165 r_symmetry_xyhbond_nbd_other 0.128 r_chiral_restr 0.094 r_ncsr_local_group_2 0.077 r_ncsr_local_group_6 0.073 r_ncsr_local_group_5 0.072 r_ncsr_local_group_4 0.071 r_symmetry_nbtor_other 0.07 r_ncsr_local_group_1 0.07 r_ncsr_local_group_3 0.065 r_bond_other_d 0.034 r_gen_planes_other 0.02 r_bond_refined_d 0.012 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11614 Nucleic Acid Atoms Solvent Atoms 1893 Heterogen Atoms 261
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MoRDa phasing