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Structure of Neuraminidase from English duck subtype N6 complexed with 30 mM sialic acid (NANA, Neu5Ac), crystal soaked for 3 hours at 277 K.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V0Z PDB ENTRY 1V0Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 293 0.15 M NACL, 20% PEG 3350 AT 293 K, pH 7.00
Crystal Properties Matthews coefficient Solvent content 2.5 50.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.993 α = 90 b = 73.464 β = 90.38 c = 107.413 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC CCD 1.2 METRE LONG SILICON SUBSTRATE, RHODIUM COATED 2004-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 SRS PX14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 33.78 99.4 0.12 4.6 3.3 112032 16.63
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 99 0.3 2.3 3.3
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 (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 PDB ENTRY 1V0Z 2 33.71 106203 5634 100 0.167 0.164 0.1742 0.207 0.1807 RANDOM 21.28
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] -2.48 -0.54 5.38 -2.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.435 r_scangle_it 4.497 r_scbond_it 3.244 r_angle_refined_deg 2.145 r_mcangle_it 1.903 r_mcbond_it 1.228 r_nbd_refined 0.249 r_symmetry_vdw_refined 0.249 r_chiral_restr 0.176 r_symmetry_hbond_refined 0.174
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.435 r_scangle_it 4.497 r_scbond_it 3.244 r_angle_refined_deg 2.145 r_mcangle_it 1.903 r_mcbond_it 1.228 r_nbd_refined 0.249 r_symmetry_vdw_refined 0.249 r_chiral_restr 0.176 r_symmetry_hbond_refined 0.174 r_xyhbond_nbd_refined 0.161 r_bond_refined_d 0.028 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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_other r_long_range_B_refined 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 12033 Nucleic Acid Atoms Solvent Atoms 1565 Heterogen Atoms 525
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling CNS phasing