☰ Navigation Tabs
Structure of a NAD-Dependent Persulfide Reductase from A. fulgidus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FX9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 100-200 mM calcium acetate, 15-20% PEG 3350 (w/w), and 1 mM DTT
Crystal Properties Matthews coefficient Solvent content 2.41 48.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.976 α = 90 b = 100.355 β = 91.894 c = 136.196 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 Cryogenically-cooled single crystal Si(220) side bounce monochromator. 2016-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.98 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3.1 40 99.7 0.119 10.3 5.2 80127 2 2 58.5513273334
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.27 0.54 2.6
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 4FX9 3.10003870577 39.4818037712 1.06887880485 79880 2782 97.8645724857 0.203188436559 0.202274311858 0.2036 0.228746674435 0.2255 55.5125936023
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 24.6929780096 f_angle_d 1.98726418669 f_chiral_restr 0.292776968012 f_bond_d 0.0239630998156 f_plane_restr 0.0119689849829
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16658 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling BALBES phasing