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The crystal structure of neuraminidase in complex with oseltamivir from A/Shanghai/2/2013 (H7N9) influenza virus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WMJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 293 0.1 M HEPES:NaOH pH 7.5, 25% PEG 1000
Crystal Properties Matthews coefficient Solvent content 2.86 56.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.436 α = 90 b = 182.436 β = 90 c = 182.436 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 CCD MARMOSAIC 300 mm CCD 2013-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 50 97.6 23.2 7.5 20042
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4wmj 2.4 40.794 1.34 20040 1031 97.47 0.1686 0.1671 0.17 0.1952 0.1953
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 f_dihedral_angle_d 13.089 f_angle_d 0.941 f_chiral_restr 0.04 f_bond_d 0.005 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3055 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 140
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing