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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.
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 6.5 291 0.1 M Sodium cacodylate pH 6.5, 18 % w/v PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 2.46 49.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.73 α = 85.964 b = 94.745 β = 89.972 c = 94.604 γ = 81.577
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 1.15 68.9 86.9 0.998 5.9 1.7 536693
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 1.15 1.17 82.3 0.325 0.6 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 1.15 68.9 536580 26885 86.847 0.197 0.1964 0.1964 0.2179 0.2179 21.743
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] -1.012 -0.045 -0.034 1.067 -0.259 -0.152
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.882 r_dihedral_angle_4_deg 14.57 r_dihedral_angle_3_deg 13.182 r_lrange_it 7.045 r_lrange_other 7.045 r_dihedral_angle_1_deg 6.752 r_scangle_it 5.962 r_scangle_other 5.961 r_scbond_it 4.606 r_scbond_other 4.605
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.882 r_dihedral_angle_4_deg 14.57 r_dihedral_angle_3_deg 13.182 r_lrange_it 7.045 r_lrange_other 7.045 r_dihedral_angle_1_deg 6.752 r_scangle_it 5.962 r_scangle_other 5.961 r_scbond_it 4.606 r_scbond_other 4.605 r_mcangle_it 4.468 r_mcangle_other 4.468 r_mcbond_it 3.531 r_mcbond_other 3.529 r_angle_other_deg 2.317 r_angle_refined_deg 1.812 r_nbd_other 0.231 r_nbd_refined 0.217 r_symmetry_nbd_other 0.214 r_symmetry_nbd_refined 0.208 r_symmetry_xyhbond_nbd_refined 0.202 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.1 r_ncsr_local_group_1 0.074 r_ncsr_local_group_4 0.072 r_ncsr_local_group_6 0.072 r_ncsr_local_group_2 0.071 r_ncsr_local_group_5 0.071 r_symmetry_nbtor_other 0.07 r_ncsr_local_group_3 0.066 r_symmetry_xyhbond_nbd_other 0.04 r_bond_other_d 0.034 r_gen_planes_other 0.024 r_gen_planes_refined 0.014 r_bond_refined_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11498 Nucleic Acid Atoms Solvent Atoms 1921 Heterogen Atoms 243
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MoRDa phasing