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The Sialidase NanJ in complex with Neu5,9Ac
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VK5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1M HEPES pH 7.5, 2.0M (NH4)2S04
Crystal Properties Matthews coefficient Solvent content 3.92 68.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.037 α = 90 b = 171.037 β = 90 c = 93.296 γ = 120
Symmetry Space Group P 64 2 2
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 2022-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 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 2.1 24.81 99.14 0.935 16.7 5.3 47174
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 2.1 2.1 0.787
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.699 24.808 22433 1156 99.143 0.187 0.1838 0.2537 0.2074 34.876
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] 0.349 0.175 0.349 -1.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.917 r_dihedral_angle_3_deg 14.424 r_dihedral_angle_1_deg 7.784 r_lrange_it 7.643 r_scangle_it 5.999 r_mcangle_it 5.09 r_scbond_it 3.916 r_dihedral_angle_2_deg 3.358 r_mcbond_it 3.272 r_angle_refined_deg 1.585
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.917 r_dihedral_angle_3_deg 14.424 r_dihedral_angle_1_deg 7.784 r_lrange_it 7.643 r_scangle_it 5.999 r_mcangle_it 5.09 r_scbond_it 3.916 r_dihedral_angle_2_deg 3.358 r_mcbond_it 3.272 r_angle_refined_deg 1.585 r_nbtor_refined 0.315 r_nbd_refined 0.225 r_symmetry_xyhbond_nbd_refined 0.196 r_symmetry_nbd_refined 0.167 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.11 r_gen_planes_refined 0.007 r_bond_refined_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3456 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing