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Crystal Structure of Porphyromonas gingivalis Sialidase (PG_0352) Bound to Neu5Ac2en (DANA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8FEB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 296 1.7 M ammonium citrate tribasic, pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.04 59.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.517 α = 90 b = 55.9 β = 115.49 c = 84.478 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 16M 2022-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
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 2.14 44 98.76 0.1458 0.1692 0.085 0.991 7.33 3.9 37392 36.56
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.14 2.217 98.3 0.904 1.042 0.5112 0.752 3.9
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 8FEB 2.14 44 1.35 37357 1784 98.5 0.1876 0.1857 0.1862 0.2272 0.2265 41.75
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 11.1588 f_angle_d 0.9079 f_chiral_restr 0.0581 f_plane_restr 0.008 f_bond_d 0.0066
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3811 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 74
Software Software Software Name Purpose PHENIX refinement Coot model building PHASER phasing xia2 data scaling DIALS data reduction xia2 data reduction Blu-Ice data collection