☰ Navigation Tabs
Structure of Atopobium parvulum SufS K235R
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5J8Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.1 294 10% PEG8000, 12% ethylene glycol, 50 mM HEPES
Crystal Properties Matthews coefficient Solvent content 2.31 46.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.744 α = 90 b = 159.262 β = 90.155 c = 178.069 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE RIGAKU RAXIS IV++ 2019-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.99 38.88 96.4 0.073 0.084 12.3 4.11 49721 68.77
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.99 3.1 93.3 0.226 0.258 5.1 4.09
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 5J8Q 2.99 38.86 1.34 49641 2005 96.26 0.2399 0.237 0.241 0.3088 0.31 61.42
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 9.6882 f_angle_d 1.3345 f_chiral_restr 0.0775 f_bond_d 0.0117 f_plane_restr 0.0084
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16502 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 120
Software Software Software Name Purpose PHENIX refinement d*TREK data scaling PDB_EXTRACT data extraction d*TREK data reduction PHASER phasing Coot model building