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flavin reductase ThdF in complex with two bound FADs in space group P212121
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4R82 experimental model PDB 4HX6 experimental model PDB 5CHO
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
Crystal Properties Matthews coefficient Solvent content 1.93 36.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.79 α = 90 b = 83.61 β = 90 c = 157.34 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 EIGER2 X CdTe 16M 2022-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9763 PETRA III, EMBL c/o DESY P14 (MX2)
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 1.14 57.3 82.4 0.088 0.089 0.015 0.999 21.5 35.2 188862 16.04
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 1.14 1.22 22.5 2.19 2.242 0.469 0.624 1.9
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 MOLECULAR REPLACEMENT FREE R-VALUE 1.14 57.29 1.34 188798 9434 82.37 0.1219 0.1209 0.1212 0.1418 0.1423 22.74
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 20.8026 f_angle_d 1.2366 f_chiral_restr 0.0885 f_plane_restr 0.0132 f_bond_d 0.0101
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4791 Nucleic Acid Atoms Solvent Atoms 569 Heterogen Atoms 462
Software Software Software Name Purpose PHENIX refinement XDS data reduction STARANISO data scaling PHASER phasing