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Crystal structure of H5N1 influenza virus hemagglutinin, strain YU562 crystal form 2
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 5.91 79.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.867 α = 90 b = 111.867 β = 90 c = 192.09 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 2010-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
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 2.95 50 99.9 0.119 10.2 12.6 29523
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 2.95 3.06 99.7 0.48 11.1
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 2.96 192.09 28027 1494 99.19 0.23891 0.23827 0.2382 0.25081 0.2499 RANDOM 49.152
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] -0.83 -0.42 -0.83 1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.632 r_dihedral_angle_4_deg 23.509 r_dihedral_angle_3_deg 18.488 r_dihedral_angle_1_deg 5.939 r_scangle_it 2.004 r_angle_refined_deg 1.287 r_scbond_it 1.168 r_mcangle_it 0.991 r_mcbond_it 0.517 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.632 r_dihedral_angle_4_deg 23.509 r_dihedral_angle_3_deg 18.488 r_dihedral_angle_1_deg 5.939 r_scangle_it 2.004 r_angle_refined_deg 1.287 r_scbond_it 1.168 r_mcangle_it 0.991 r_mcbond_it 0.517 r_chiral_restr 0.086 r_bond_refined_d 0.009 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 2555 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 38
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction