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Crystal structure of H5N1 influenza virus hemagglutinin, strain YU562 crystal form 1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 291 1.62M ammonium sulfate, 0.1M sodium cacodylate pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 4.19 70.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.552 α = 90 b = 112.552 β = 90 c = 134.689 γ = 120
Symmetry Space Group P 3 2 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 CCD MAR CCD 2010-08-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0000 APS 22-BM
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 3.1 50 99.9 0.151 6.1 11 18334
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 3.1 3.21 100 0.459 9.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.1 134.69 17391 940 99.69 0.21949 0.21714 0.2153 0.26443 0.2596 RANDOM 37.214
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] 2.64 1.32 2.64 -3.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.871 r_dihedral_angle_3_deg 19.01 r_dihedral_angle_4_deg 16.818 r_dihedral_angle_1_deg 5.777 r_scangle_it 1.714 r_angle_refined_deg 1.117 r_scbond_it 0.997 r_mcangle_it 0.78 r_mcbond_it 0.401 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.871 r_dihedral_angle_3_deg 19.01 r_dihedral_angle_4_deg 16.818 r_dihedral_angle_1_deg 5.777 r_scangle_it 1.714 r_angle_refined_deg 1.117 r_scbond_it 0.997 r_mcangle_it 0.78 r_mcbond_it 0.401 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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 3792 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 52
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction