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Structure of F420-H2 Dependent Oxidoreductase (FDOR-A) MSMEG_2027 in complex with F420
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Y9I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.4 291.15 0.07 M citrate, 0.03 M bis-tris propane, 16% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.3 46.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.364 α = 90 b = 63.022 β = 90 c = 65.366 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 2017-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953729987144 Australian Synchrotron 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 1.67 32.68 99.8 0.173 0.183 0.078 0.996 11.8 10.6 17596 19.79
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 1.7 99.9 1.556 0.511 0.91 1.9 10.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4Y9I 1.67 32.68 1.34 17438 907 99.22 0.2022 0.2002 0.201 0.2409 0.2424
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 20.681 f_angle_d 0.683 f_chiral_restr 0.046 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1152 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 71
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building