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NanH sialidase from C. perfringens in complex with Sialyl LacNAc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8UB5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.1 M HEPES, PH 7.5 2.0 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.27 45.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.745 α = 90 b = 64.558 β = 103.01 c = 66.342 γ = 90
Symmetry Space Group C 1 2 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 PILATUS 200K 2021-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-002 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.18 29.74 96.93 0.991 12.9 4.2 21322
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.18 2.23 0.813
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 2.18 29.74 18800 984 96.93 0.1765 0.17313 0.1732 0.23984 0.24 RANDOM 32.846
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] -0.08 0.04 0.05 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.776 r_dihedral_angle_1_deg 8.07 r_dihedral_angle_2_deg 6.909 r_long_range_B_refined 6.168 r_mcangle_it 4.114 r_scbond_it 3.883 r_mcbond_it 3.144 r_angle_refined_deg 1.796 r_chiral_restr 0.129 r_gen_planes_refined 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.776 r_dihedral_angle_1_deg 8.07 r_dihedral_angle_2_deg 6.909 r_long_range_B_refined 6.168 r_mcangle_it 4.114 r_scbond_it 3.883 r_mcbond_it 3.144 r_angle_refined_deg 1.796 r_chiral_restr 0.129 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2816 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing