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Effects of zinc ion on oligomerization and pH stability of influenza virus hemagglutinin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 297 PEG 2000, Tris, DMSO
Crystal Properties Matthews coefficient Solvent content 4.28 71.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 215.71 α = 90 b = 124.27 β = 102.909 c = 214.53 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS 6M 2015-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 3.24 48.75 99.91 0.2875 0.07844 0.988 7.73 13.3 172506 54.83
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.24 3.356 100 0.728 0.2064 0.92 3.23
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 4EDB 3.24 48.75 1.35 172506 3926 99.92 0.2661 0.2654 0.2654 0.2948 0.2947 74.73
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 15.0833 f_angle_d 1.6707 f_chiral_restr 0.088 f_bond_d 0.0128 f_plane_restr 0.0123
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23024 Nucleic Acid Atoms Solvent Atoms 428 Heterogen Atoms 961
Software Software Software Name Purpose ADSC data collection PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing