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Crystal structure of the 2009 H1N1 influenza virus hemagglutinin receptor-binding domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RUY PDB entry 1RUY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 PEG 2000MME, Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.09 41.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.857 α = 90 b = 74.065 β = 94.73 c = 75.18 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 315r 2010-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0 ALS 8.2.1
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 2.1 40 100 0.127 8.3 5 25593 25588 12.73 19.628
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) 2.1 2.18 100 0.373 3.83 3.9 2518
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1RUY 2.09 39.72 25564 25564 1306 98.84 0.178 0.178 0.177 0.1793 0.206 0.2071 RANDOM 19.628
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] 0.02 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.812 r_dihedral_angle_4_deg 21.407 r_dihedral_angle_3_deg 13.769 r_dihedral_angle_1_deg 6.291 r_scangle_it 2.3 r_scbond_it 1.341 r_angle_refined_deg 1.074 r_mcangle_it 0.908 r_mcbond_it 0.458 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.812 r_dihedral_angle_4_deg 21.407 r_dihedral_angle_3_deg 13.769 r_dihedral_angle_1_deg 6.291 r_scangle_it 2.3 r_scbond_it 1.341 r_angle_refined_deg 1.074 r_mcangle_it 0.908 r_mcbond_it 0.458 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3374 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 36
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction SERGUI data collection HKL-2000 data reduction HKL-2000 data scaling