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Crystal structure of the haemagglutinin from a transmissible H10N7 seal influenza virus isolated in Netherland
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D00
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 26%-31% PEG600, 0.1M HEPES pH7.5 or 0.1M tris pH8.0
Crystal Properties Matthews coefficient Solvent content 3.12 60.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.38 α = 90 b = 214.95 β = 97.58 c = 74.67 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 PIXEL DECTRIS PILATUS3 6M 2017-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.84 51.48 99.1 1 10.8 3.3 171611
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.84 1.87 99.9 0.5 3.4
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 4d00 1.84 51.48 171552 8385 99.04 0.233 0.232 0.2275 0.2527 0.2481 RANDOM 49.2398
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] -0.53 -1.08 -0.25 1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.396 r_dihedral_angle_3_deg 12.453 r_dihedral_angle_4_deg 10.957 r_dihedral_angle_1_deg 5.434 r_mcangle_it 3.889 r_angle_other_deg 3.86 r_mcbond_it 2.71 r_mcbond_other 2.71 r_angle_refined_deg 1.057 r_chiral_restr 0.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.396 r_dihedral_angle_3_deg 12.453 r_dihedral_angle_4_deg 10.957 r_dihedral_angle_1_deg 5.434 r_mcangle_it 3.889 r_angle_other_deg 3.86 r_mcbond_it 2.71 r_mcbond_other 2.71 r_angle_refined_deg 1.057 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_gen_planes_other 0.003 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11343 Nucleic Acid Atoms Solvent Atoms 735 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement DIALS data reduction xia2 data scaling REFMAC phasing