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Structure of Tannerella forsythia endopeptidase O (TfPepO)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DWB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.3 M sodium fluoride, 0.3 M sodium bromide, 0.3 M sodium iodide, 0.1M buffer system containing imidazole / MES mix, 40% (v/v) ethylene glycol, 20% (w/v) PEG 8000, pH=6.5
Crystal Properties Matthews coefficient Solvent content 2.67 53.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.414 α = 90 b = 95.414 β = 90 c = 301.9 γ = 120
Symmetry Space Group P 32 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 193 PIXEL DECTRIS PILATUS 6M 2020-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1 ELETTRA 11.2C
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 1.8 48.8 99.96 0.07979 16.92 9.3 148384 29.81
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 1.8 1.86 99.99 1.132 9.5
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.8 48.75 1.34 148368 7428 99.97 0.1955 0.1941 0.1936 0.2233 0.2228 RANDOM 35.59
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 16.1272 f_angle_d 0.9727 f_chiral_restr 0.0584 f_bond_d 0.0089 f_plane_restr 0.0085
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10482 Nucleic Acid Atoms Solvent Atoms 799 Heterogen Atoms 153
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling MoRDa phasing