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Crystal structure of a H7 influenza virus hemagglutinin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TI8 PDB Entry 1TI8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Microbatch under oil 7.2 298 20% PEG 3350, 0.2 M magnesium chloride at pH 7.2, Microbatch under oil, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.89 57.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.882 α = 90 b = 115.434 β = 90 c = 250.967 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 IMAGE PLATE MAR scanner 300 mm plate 2008-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.6 50 99.2 0.106 39.6 7.2 62462 61857
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.6 2.69 99 0.413 2 6.2
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 PDB Entry 1TI8 2.6 50 57285 3053 99.29 0.21879 0.21685 0.2214 0.25559 0.2599 RANDOM 16.926
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] 1.81 -0.43 -1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.433 r_dihedral_angle_3_deg 15.466 r_dihedral_angle_4_deg 15.11 r_dihedral_angle_1_deg 5.085 r_scangle_it 3.708 r_scbond_it 2.321 r_mcangle_it 1.239 r_angle_refined_deg 0.905 r_mcbond_it 0.688 r_chiral_restr 0.058
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.433 r_dihedral_angle_3_deg 15.466 r_dihedral_angle_4_deg 15.11 r_dihedral_angle_1_deg 5.085 r_scangle_it 3.708 r_scbond_it 2.321 r_mcangle_it 1.239 r_angle_refined_deg 0.905 r_mcbond_it 0.688 r_chiral_restr 0.058 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11357 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 140
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling