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H5 Haemagglutinin in Complex with Sialyl-Lewis X
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IBX PDB ENTRY 2IBX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1 M HEPES, PH 7.0, 0.05 M MGCL2, 28 - 30 % PEG 550 MME
Crystal Properties Matthews coefficient Solvent content 4.04 70
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 175.56 α = 90 b = 101.36 β = 111.29 c = 161.2 γ = 90
Symmetry Space Group C 1 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 PIXEL DECTRIS PILATUS 2M 2012-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 2.4 150.76 75.6 0.08 8.2 3.3 77719 3 53.2
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 2IBX 2.4 37.15 73837 3882 75.64 0.2387 0.23777 0.2409 0.25632 0.258 RANDOM 47.1
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] -0.11 0.21 -0.65 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.912 r_dihedral_angle_3_deg 17.569 r_dihedral_angle_4_deg 16.025 r_dihedral_angle_1_deg 5.225 r_angle_refined_deg 0.997 r_angle_other_deg 0.72 r_scbond_it 0.594 r_mcangle_it 0.287 r_mcbond_it 0.154 r_mcbond_other 0.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.912 r_dihedral_angle_3_deg 17.569 r_dihedral_angle_4_deg 16.025 r_dihedral_angle_1_deg 5.225 r_angle_refined_deg 0.997 r_angle_other_deg 0.72 r_scbond_it 0.594 r_mcangle_it 0.287 r_mcbond_it 0.154 r_mcbond_other 0.154 r_chiral_restr 0.055 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11595 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 339
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing