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Structure of Neuraminidase from English duck subtype N6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NNA PDB ENTRY 1NNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 20 PERCENT (W/V) PEG 3350, 150 MM NACL
Crystal Properties Matthews coefficient Solvent content 2.48 50.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.482 α = 90 b = 73.755 β = 90.37 c = 106.809 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 MARRESEARCH 1995-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX7.2 SRS PX7.2
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 1.84 19.96 100 0.07 7.8 6.7 127094 18.1
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 1.84 1.89 100 0.16 3.4 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 1NNA 1.84 19.96 127094 6696 100 0.151 0.149 0.1498 0.19 0.1873 RANDOM 15.07
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] -1.02 0.04 2.34 -1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.186 r_dihedral_angle_4_deg 16.132 r_dihedral_angle_3_deg 12.534 r_dihedral_angle_1_deg 7.18 r_scangle_it 2.84 r_scbond_it 1.828 r_angle_refined_deg 1.428 r_mcangle_it 1.038 r_mcbond_it 0.656 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.186 r_dihedral_angle_4_deg 16.132 r_dihedral_angle_3_deg 12.534 r_dihedral_angle_1_deg 7.18 r_scangle_it 2.84 r_scbond_it 1.828 r_angle_refined_deg 1.428 r_mcangle_it 1.038 r_mcbond_it 0.656 r_nbtor_refined 0.306 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.188 r_symmetry_hbond_refined 0.145 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.101 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 12036 Nucleic Acid Atoms Solvent Atoms 1798 Heterogen Atoms 513
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing