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Three dimensional structure of a novel influenza hemagglutinin tri-stalk protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HTM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 294 2.0 M ammonium sulfate and 0.1 M Bis-Tris, pH 5.5, protein 10 mg/mL
Crystal Properties Matthews coefficient Solvent content 2.66 53.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.8 α = 90 b = 41.8 β = 90 c = 90.12 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 CCD MARMOSAIC 225 mm CCD RH-COATED TOROIDAL SI MIRROR 2015-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.00000 MAX II I911-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 23.12 99.7 0.063 10 3.7 9803 22.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.79 100 0.664 1.8 3.7
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 1HTM 1.7 23.12 9323 473 99.47 0.17959 0.17771 0.1902 0.21914 0.2322 RANDOM 36.711
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] -0.01 -0.01 -0.01 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.114 r_dihedral_angle_4_deg 17.379 r_dihedral_angle_3_deg 13.178 r_long_range_B_refined 8.298 r_long_range_B_other 8.298 r_scangle_other 6.774 r_dihedral_angle_1_deg 5.499 r_mcangle_other 5.409 r_mcangle_it 5.408 r_scbond_it 4.544
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.114 r_dihedral_angle_4_deg 17.379 r_dihedral_angle_3_deg 13.178 r_long_range_B_refined 8.298 r_long_range_B_other 8.298 r_scangle_other 6.774 r_dihedral_angle_1_deg 5.499 r_mcangle_other 5.409 r_mcangle_it 5.408 r_scbond_it 4.544 r_scbond_other 4.536 r_mcbond_it 3.643 r_mcbond_other 3.628 r_angle_refined_deg 2.009 r_angle_other_deg 1.084 r_chiral_restr 0.129 r_bond_refined_d 0.024 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 537 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing