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Treponema denticola OppA complexed with SSGTQSI and SASSSS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 291.15 0.2 M Ammonium chloride, pH 6.3, 20% (w/v) PEG3350, 20 mg/mL TdOppA supplemented with 20 mg/mL DKEVMGILSTALRSMLLTGRDEHGDE (SAR) peptide
Crystal Properties Matthews coefficient Solvent content 2.2 43.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.51 α = 90 b = 50.01 β = 108.78 c = 110.74 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 PIXEL DECTRIS EIGER X 9M 2022-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9537 CLSI 08ID-1
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 1.74 45.14 90.57 0.02959 0.04185 0.02959 0.999 8.57 2 104773 34.63
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.74 1.8 49.71 1.352 0.131 0.48 2
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 THROUGHOUT 1.74 45.14 1.34 104126 5211 90.58 0.2011 0.1993 0.2025 0.2355 0.2385 RANDOM
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 6.481 f_angle_d 0.96 f_chiral_restr 0.057 f_plane_restr 0.01 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9045 Nucleic Acid Atoms Solvent Atoms 501 Heterogen Atoms 9
Software Software Software Name Purpose MxDC data collection autoPROC data processing SCALA data scaling REFMAC phasing PHENIX model building PHENIX refinement