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GH31 alpha-N-acetylgalactosaminidase from Enterococcus faecalis in complex with N-acetylgalactosamine
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, 5 mM N-acetylgalactosamine
Crystal Properties Matthews coefficient Solvent content 2.38 48.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.596 α = 90 b = 83.233 β = 90 c = 147.787 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 6M 2020-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 50 99.8 0.077 0.998 13.8 6 80809
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 1.9 2 99.4 0.448 0.844 3.6
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 1.9 40.091 80706 4011 99.722 0.219 0.217 0.2236 0.2611 0.2673 30.848
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] -1.58 -0.078 1.658
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.926 r_dihedral_angle_4_deg 17.388 r_dihedral_angle_3_deg 14.369 r_dihedral_angle_1_deg 7.82 r_lrange_it 5.626 r_lrange_other 5.608 r_scangle_it 4.169 r_scangle_other 4.168 r_mcangle_other 3.925 r_mcangle_it 3.924
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.926 r_dihedral_angle_4_deg 17.388 r_dihedral_angle_3_deg 14.369 r_dihedral_angle_1_deg 7.82 r_lrange_it 5.626 r_lrange_other 5.608 r_scangle_it 4.169 r_scangle_other 4.168 r_mcangle_other 3.925 r_mcangle_it 3.924 r_scbond_it 2.886 r_scbond_other 2.885 r_mcbond_it 2.849 r_mcbond_other 2.847 r_angle_refined_deg 1.682 r_angle_other_deg 1.337 r_nbd_other 0.275 r_nbd_refined 0.201 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.171 r_symmetry_nbd_refined 0.17 r_xyhbond_nbd_refined 0.157 r_metal_ion_refined 0.117 r_symmetry_xyhbond_nbd_refined 0.099 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.079 r_symmetry_xyhbond_nbd_other 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7090 Nucleic Acid Atoms Solvent Atoms 309 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing