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Enterococcus faecalis GH31 alpha-N-acetylgalactosaminidase D455N in complex with Tn antigen
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6M76
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 25% PEG3350, 0.2 M ammonium citrate
Crystal Properties Matthews coefficient Solvent content 2.39 48.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.706 α = 90 b = 82.973 β = 90 c = 148.58 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 PILATUS3 S 2M 2020-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 1.63 50 100 0.068 0.07 0.019 1 23.8 13.1 127951
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 1.63 1.72 100 0.961 0.287 0.809 2.6 12.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6M76 1.63 46.04 127854 6325 99.986 0.178 0.1772 0.1867 0.2004 0.2078 27.096
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] 2.041 -2.18 0.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.327 r_dihedral_angle_4_deg 19.223 r_dihedral_angle_3_deg 13.187 r_dihedral_angle_1_deg 7.276 r_lrange_it 4.622 r_lrange_other 4.563 r_scangle_it 2.343 r_scangle_other 2.343 r_angle_refined_deg 1.629 r_mcangle_other 1.615
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.327 r_dihedral_angle_4_deg 19.223 r_dihedral_angle_3_deg 13.187 r_dihedral_angle_1_deg 7.276 r_lrange_it 4.622 r_lrange_other 4.563 r_scangle_it 2.343 r_scangle_other 2.343 r_angle_refined_deg 1.629 r_mcangle_other 1.615 r_mcangle_it 1.614 r_scbond_it 1.5 r_scbond_other 1.5 r_angle_other_deg 1.435 r_mcbond_it 1.035 r_mcbond_other 1.031 r_nbd_refined 0.206 r_symmetry_nbd_refined 0.196 r_symmetry_nbd_other 0.177 r_nbtor_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.152 r_nbd_other 0.131 r_metal_ion_refined 0.122 r_xyhbond_nbd_refined 0.119 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7036 Nucleic Acid Atoms Solvent Atoms 558 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing Coot model building