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Structure of Neuraminidase from English duck subtype N6 complexed with 30 mM sialic acid (NANA, Neu5Ac), crystal soaked for 43 hours at 291 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 2.49 50.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.478 α = 90 b = 73.995 β = 90.5 c = 106.465 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 IMAGE PLATE MAR scanner 345 mm plate CONFOCAL OSMIC BLUE 2004-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200H
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 2.08 30.43 98.2 0.09 7.9 2.2 98861 18.85
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 2.08 2.19 92.3 0.27 2.7 2.1
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 2.08 30.43 93358 4913 98 0.153 0.15 0.1605 0.195 0.2078 RANDOM 19.39
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] -1.59 -0.43 2.89 -1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.92 r_scangle_it 4.289 r_scbond_it 2.998 r_angle_refined_deg 2.042 r_mcangle_it 1.752 r_mcbond_it 1.088 r_nbd_refined 0.355 r_symmetry_vdw_refined 0.276 r_chiral_restr 0.199 r_xyhbond_nbd_refined 0.147
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.92 r_scangle_it 4.289 r_scbond_it 2.998 r_angle_refined_deg 2.042 r_mcangle_it 1.752 r_mcbond_it 1.088 r_nbd_refined 0.355 r_symmetry_vdw_refined 0.276 r_chiral_restr 0.199 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.122 r_bond_refined_d 0.022 r_gen_planes_refined 0.014 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 1723 Heterogen Atoms 529
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling CNS phasing