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Enterococcus faecalis GH31 alpha-N-acetylgalactosaminidase D455A in complex with p-nitrophenyl alpha-N-acetylgalactosaminide
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 2.34 47.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.875 α = 90 b = 83.394 β = 90 c = 146.329 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 1.42 50 98 0.067 0.069 0.019 1 24.5 13.3 184729
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 1.42 1.5 94.7 1.044 0.29 0.766 2.7 13.5
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 1.42 42.139 184632 9317 97.837 0.175 0.1743 0.1817 0.1963 0.2012 22.221
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] -0.588 -0.524 1.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.84 r_dihedral_angle_4_deg 16.405 r_dihedral_angle_3_deg 12.396 r_dihedral_angle_1_deg 7.222 r_lrange_it 5.159 r_lrange_other 5.031 r_angle_refined_deg 1.726 r_angle_other_deg 1.548 r_scangle_it 1.387 r_scangle_other 1.387
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.84 r_dihedral_angle_4_deg 16.405 r_dihedral_angle_3_deg 12.396 r_dihedral_angle_1_deg 7.222 r_lrange_it 5.159 r_lrange_other 5.031 r_angle_refined_deg 1.726 r_angle_other_deg 1.548 r_scangle_it 1.387 r_scangle_other 1.387 r_mcangle_it 0.945 r_mcangle_other 0.944 r_scbond_it 0.921 r_scbond_other 0.921 r_mcbond_other 0.543 r_mcbond_it 0.542 r_nbd_refined 0.211 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.186 r_nbd_other 0.185 r_symmetry_nbd_refined 0.159 r_symmetry_xyhbond_nbd_refined 0.135 r_symmetry_xyhbond_nbd_other 0.125 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.014 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 7020 Nucleic Acid Atoms Solvent Atoms 792 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing Coot model building