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Crystal structure of viperin with bound [4Fe-4S] cluster and S-adenosylhomocysteine (SAH)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 100 mM HEPES, pH 6.8 - 7.6, 10 - 30 % (w/v) PEG MME 2000, and 5 mM SAH
Crystal Properties Matthews coefficient Solvent content 2.1 41.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.934 α = 90 b = 73.854 β = 90 c = 141.872 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 PILATUS 6M-F 2015-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9793 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.97 50 95 0.079 12.6 5.2 42331
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2.04 96.7 0.578 2.4 4.9
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 SAD FREE R-VALUE 1.972 46.065 1.37 42302 2110 95.1 0.1571 0.1549 0.1567 0.1997 0.2009
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 16.694 f_angle_d 2.008 f_chiral_restr 0.055 f_bond_d 0.015 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4175 Nucleic Acid Atoms Solvent Atoms 402 Heterogen Atoms 68
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling Coot model building SHELXD phasing PHENIX phasing HKL-2000 data collection