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Treponema denticola OppA complexed with LSLNSS and SAKASA
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 291.15 0.2 M Ammonium iodide, 20% (w/v) PEG3350, 20 mg/mL TdOppA, supplemented with 40 mg/mL DKEVMGILSTALRSMLLTGRDEHGDE (SAR) peptide
Crystal Properties Matthews coefficient Solvent content 2.3 46.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.29 α = 90 b = 50.95 β = 109.42 c = 112 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 1.87 45.93 99.88 0.09806 0.1064 0.0409 0.998 10.14 6.7 97540 37.78
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.937 99.62 0.142 5.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 1.87 45.93 92735 4811 99.91 0.20891 0.20729 0.2175 0.24163 0.245 RANDOM 27.401
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] 2.28 -0.58 0.45 -1.86
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9116 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 18
Software Software Software Name Purpose MxDC data collection autoPROC data reduction SCALA data scaling PHASER phasing PHENIX model building PHENIX refinement