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flavin reductase ThdF in complex with NAD and FAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9FD4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 D12 JCSG++ (Jena Bioscience); 40 mM KH2PO4, 20 % (v/v) glycerol, 16 % (w/v) PEG 8000;
18 mg/mL ThdF (50 mM HEPES pH 7.0, 20 mM NaCl, 1 mM DTT), 1:1800 (mass ratio) elastase added;
600 nL protein + 300 nL reservoir;
soaking with 250 nL 100 mM NADH and 250 nL 500 mM dithionite
Crystal Properties Matthews coefficient Solvent content 1.95 36.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.76 α = 90 b = 83.48 β = 90 c = 159.06 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2023-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9762 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.43 73.92 80.3 0.095 0.098 0.027 0.999 14.9 13.5 95935 18.12
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.43 1.55 18.6 1.901 1.974 0.529 0.594 1.5 13.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 1.43 45.74 1.34 95908 4919 80.27 0.1477 0.1458 0.1519 0.1822 0.1829
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 21.091 f_angle_d 0.959 f_chiral_restr 0.068 f_plane_restr 0.008 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4801 Nucleic Acid Atoms Solvent Atoms 659 Heterogen Atoms 388
Software Software Software Name Purpose PHENIX refinement XDS data reduction STARANISO data scaling PHENIX phasing