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Crystal structure of the haemagglutinin from a H10N7 seal influenza virus isolated in Germany in complex with human receptor analogue, 6'-SLN
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 2%-4% PEG6000, 0.1M HEPES pH7.0
Crystal Properties Matthews coefficient Solvent content 3.5 65.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.815 α = 90 b = 214.138 β = 101.07 c = 158.394 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 PILATUS 6M-F 2017-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
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 2.6 68.52 99 0.998 8.4 3.2 138258
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 2.6 2.64 0.576
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 2.6 68.52 138249 7070 98.95 0.2412 0.2393 0.2328 0.276 0.2648 RANDOM 91.219
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] -0.02 -0.32 0.31 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.48 r_dihedral_angle_3_deg 16.187 r_dihedral_angle_4_deg 14.196 r_mcangle_it 8.538 r_dihedral_angle_1_deg 6.03 r_mcbond_it 5.59 r_mcbond_other 5.59 r_angle_other_deg 4.196 r_angle_refined_deg 1.814 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.48 r_dihedral_angle_3_deg 16.187 r_dihedral_angle_4_deg 14.196 r_mcangle_it 8.538 r_dihedral_angle_1_deg 6.03 r_mcbond_it 5.59 r_mcbond_other 5.59 r_angle_other_deg 4.196 r_angle_refined_deg 1.814 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_other 0.007 r_gen_planes_refined 0.005 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22893 Nucleic Acid Atoms Solvent Atoms 370 Heterogen Atoms 422
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction Aimless data scaling PHASER phasing