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Structure of Neuraminidase Subtype N9 Complexed with 30 MM Sialic Acid (NANA, NEU5AC), Crystal Soaked for 3 Hours at 291 K.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NN9 PDB ENTRY 7NN9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.8 PROTEIN WAS CRYSTALLISED FROM 1.9M POTASSIUM PHOSPHATE PH 6.8, THEN SOAKED FOR 3 HOURS IN 30 MM NEU5AC
Crystal Properties Matthews coefficient Solvent content 2.94 58.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.336 α = 90 b = 181.336 β = 90 c = 181.336 γ = 90
Symmetry Space Group I 4 3 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 IMAGE PLATE MAR scanner 345 mm plate CONFOCAL OSMIC BLUE 2004-06-10 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 2.15 38.66 100 0.12 5.5 9.9 27874 16.57
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 2.15 2.21 100 0.27 2.8 9.4
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 7NN9 2.15 30.1 26444 1401 99.9 0.16 0.158 0.1594 0.205 0.2056 RANDOM 12.2
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.305 r_dihedral_angle_4_deg 18.688 r_dihedral_angle_3_deg 13.154 r_dihedral_angle_1_deg 7.647 r_scangle_it 2.911 r_scbond_it 1.98 r_angle_refined_deg 1.602 r_mcangle_it 1.057 r_mcbond_it 0.689 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.305 r_dihedral_angle_4_deg 18.688 r_dihedral_angle_3_deg 13.154 r_dihedral_angle_1_deg 7.647 r_scangle_it 2.911 r_scbond_it 1.98 r_angle_refined_deg 1.602 r_mcangle_it 1.057 r_mcbond_it 0.689 r_nbtor_refined 0.31 r_nbd_refined 0.287 r_symmetry_vdw_refined 0.19 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.111 r_symmetry_hbond_refined 0.092 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other 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 3067 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 190
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing