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NAD+-dependent fungal formate dehydrogenase from Chaetomium thermophilum: A complex of N120C mutant protein 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 7.5 291 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 7.5, 10 % w/v PEG 1000, 10 % w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.45 49.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.731 α = 85.627 b = 94.606 β = 89.88 c = 94.614 γ = 81.618
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 1.12 63.93 82.1 0.998 5.7 1.7 548213 15.7
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 1.12 1.14 53.2 0.291 0.8 1.4
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 1.12 63.93 548212 27331 82.101 0.208 0.2069 0.2069 0.2276 0.2277 18.109
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] -0.172 -0.052 -0.041 0.793 0.069 -0.651
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.156 r_dihedral_angle_4_deg 14.201 r_dihedral_angle_3_deg 13.08 r_dihedral_angle_1_deg 6.819 r_lrange_other 6.113 r_lrange_it 6.112 r_scangle_it 5.084 r_scangle_other 5.083 r_scbond_it 3.963 r_scbond_other 3.963
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.156 r_dihedral_angle_4_deg 14.201 r_dihedral_angle_3_deg 13.08 r_dihedral_angle_1_deg 6.819 r_lrange_other 6.113 r_lrange_it 6.112 r_scangle_it 5.084 r_scangle_other 5.083 r_scbond_it 3.963 r_scbond_other 3.963 r_mcangle_it 3.785 r_mcangle_other 3.785 r_mcbond_it 3.013 r_mcbond_other 3.013 r_angle_other_deg 2.339 r_angle_refined_deg 1.92 r_symmetry_nbd_refined 0.253 r_nbd_other 0.248 r_symmetry_xyhbond_nbd_refined 0.248 r_nbd_refined 0.216 r_symmetry_nbd_other 0.212 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.163 r_xyhbond_nbd_other 0.135 r_chiral_restr 0.103 r_ncsr_local_group_5 0.074 r_ncsr_local_group_6 0.072 r_symmetry_nbtor_other 0.071 r_ncsr_local_group_4 0.069 r_ncsr_local_group_1 0.066 r_ncsr_local_group_2 0.066 r_ncsr_local_group_3 0.063 r_bond_other_d 0.034 r_gen_planes_other 0.032 r_gen_planes_refined 0.018 r_bond_refined_d 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11503 Nucleic Acid Atoms Solvent Atoms 1759 Heterogen Atoms 256
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MoRDa phasing