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Crystal Structure of the refolded Hemagglutinin head domain of Influenza A virus A/Ohio/09/2015
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UYN pdb entry 6uynA as per Morda
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 287 RigakuReagents JCSG+ screen, condition a10: 200mM potassium formate, 20% (w/V) PEG 3350: InvbR.18715.a.TK11.PD38402 at 4.1mg/ml: tray: 314055a1: cryo: 20% EG: puck vjj0-9.
Crystal Properties Matthews coefficient Solvent content 1.96 37.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.67 α = 90 b = 61.12 β = 90 c = 89.34 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX MX-300 Beryllium Lenses 2021-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.6 50 99.2 0.074 0.081 0.999 16.87 5.99 27045 21.663
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.64 99.9 0.597 0.656 0.859 3.4 6.005
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE pdb entry 6uynA as per Morda 1.6 36.06 1.35 27043 1937 99.23 0.1626 0.1597 0.1597 0.1997 0.1996 0 17.08
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 11.5389 f_angle_d 0.9172 f_chiral_restr 0.0602 f_bond_d 0.0074 f_plane_restr 0.0069
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1649 Nucleic Acid Atoms Solvent Atoms 269 Heterogen Atoms 4
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MoRDa phasing PHENIX model building Coot model building