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Crystal Structure of B/Perth Neuraminidase in complex with Peramivir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K36 PDB ENTRY 3K36
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 281.15 0.2M NaNO3, 20% w/v PEG3350, 0.1M bis-tris propane, pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 281.15K
Crystal Properties Matthews coefficient Solvent content 2.33 47.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.645 α = 90 b = 88.645 β = 90 c = 207.523 γ = 90
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 QUANTUM 210r BEAMLINE OPTICS 2008-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.95364 Australian Synchrotron MX1
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 40.76 87.6 0.128 10.1 4.6 47163 47163 -1 -1 12.108
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) 2 2.11 90.9 0.335 3.8 4.1 7141
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3K36 2 40.76 44772 44772 2388 87.65 0.17462 0.17124 0.1733 0.23732 0.2406 RANDOM 12.27
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] -1.22 -1.22 2.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.677 r_dihedral_angle_3_deg 17.974 r_dihedral_angle_4_deg 16.49 r_dihedral_angle_1_deg 7.638 r_scangle_it 2.855 r_scbond_it 1.946 r_angle_refined_deg 1.625 r_mcangle_it 1.135 r_mcbond_it 0.629 r_chiral_restr 0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.677 r_dihedral_angle_3_deg 17.974 r_dihedral_angle_4_deg 16.49 r_dihedral_angle_1_deg 7.638 r_scangle_it 2.855 r_scbond_it 1.946 r_angle_refined_deg 1.625 r_mcangle_it 1.135 r_mcbond_it 0.629 r_chiral_restr 0.115 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6012 Nucleic Acid Atoms Solvent Atoms 787 Heterogen Atoms 104
Software Software Software Name Purpose Blu-Ice data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling