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Crystal structure of H8 haemagglutinin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JSD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.1 M HEPES pH 7.0, 20-22% PEG3350,
0.2 M lithium citrate
Crystal Properties Matthews coefficient Solvent content 3 58.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.739 α = 90 b = 98.739 β = 90 c = 350.383 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 PIXEL DECTRIS PILATUS 6M 2014-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 83.07 99.8 0.998 11.4 6.1 44838
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 0.786
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 1jsd 2 83.07 44635 2249 99.18 0.2259 0.2242 0.2238 0.2565 0.2536 RANDOM 44.238
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 -0.02 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.167 r_dihedral_angle_4_deg 17.544 r_dihedral_angle_3_deg 15.142 r_dihedral_angle_1_deg 7.156 r_angle_other_deg 4.072 r_mcangle_it 2.056 r_angle_refined_deg 1.682 r_mcbond_it 1.25 r_mcbond_other 1.25 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.167 r_dihedral_angle_4_deg 17.544 r_dihedral_angle_3_deg 15.142 r_dihedral_angle_1_deg 7.156 r_angle_other_deg 4.072 r_mcangle_it 2.056 r_angle_refined_deg 1.682 r_mcbond_it 1.25 r_mcbond_other 1.25 r_chiral_restr 0.078 r_bond_refined_d 0.013 r_gen_planes_other 0.004 r_gen_planes_refined 0.003 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3893 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 169
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SCALA data scaling PHASER phasing xia2 data reduction