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Treponema denticola OppA complexed with TSGDAA and ATSAAA
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, HANGING DROP 4.2 291.15 0.1 M Na2HPO4:citirc acid, pH 4.2, 0.2 M NaCl, 22% (w/v) PEG3350, 15% (w/v) GOL, 0.05 M L-Lys, 20 mg/mL TdOppA
Crystal Properties Matthews coefficient Solvent content 2.26 45.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.32 α = 90 b = 108.3 β = 90 c = 213.26 γ = 90
Symmetry Space Group P 21 21 21
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 2 48.33 99.93 0.05334 0.07543 0.05334 0.996 6.78 2 159387 43.08
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.072 99.97 0.7828 0.7828 0.133 2
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 2 48.33 79804 3997 99.93 0.23959 0.23809 0.2315 0.26756 0.2302 RANDOM 58.846
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] -0.13 1.06 -0.93
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9106 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 1
Software Software Software Name Purpose MxDC data collection autoPROC data reduction SCALA data scaling REFMAC phasing PHENIX model building PHENIX refinement