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Crystal structure of S9-3-37 bound to H5 influenza hemagglutinin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FK0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% PEG 6000, 0.1 M HEPES pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.87 68.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.269 α = 90 b = 157.269 β = 90 c = 345.167 γ = 120
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 2018-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.9 50 100 0.23 0.05 0.99 16.2 20.2 36791 62
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3 100 1.26 0.28 0.8 2 21
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2FK0 2.9 45.44 34961 1787 99.94 0.20737 0.20535 0.24774 0.2259 RANDOM 75.182
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] 0.47 0.24 0.47 -1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.415 r_dihedral_angle_3_deg 18.699 r_dihedral_angle_4_deg 18.6 r_dihedral_angle_1_deg 7.016 r_long_range_B_refined 6.435 r_long_range_B_other 6.435 r_scangle_other 2.808 r_mcangle_it 1.872 r_mcangle_other 1.872 r_scbond_it 1.605
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.415 r_dihedral_angle_3_deg 18.699 r_dihedral_angle_4_deg 18.6 r_dihedral_angle_1_deg 7.016 r_long_range_B_refined 6.435 r_long_range_B_other 6.435 r_scangle_other 2.808 r_mcangle_it 1.872 r_mcangle_other 1.872 r_scbond_it 1.605 r_scbond_other 1.605 r_angle_refined_deg 1.106 r_mcbond_it 1.081 r_mcbond_other 1.081 r_angle_other_deg 0.399 r_chiral_restr 0.045 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7392 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 147
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing