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Crystal structure of human 1G01 Fab in complex with influenza virus neuraminidase from A/California/04/2009 (H1N1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NSS 3NSS, 5ITB, 4FQL experimental model PDB 5ITB 3NSS, 5ITB, 4FQL experimental model PDB 4FQL 3NSS, 5ITB, 4FQL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1 M Tris, pH 8.5, 10% (v/v) glycerol, 20% (w/v) PEG300, 5% (w/v) PEG8000
Crystal Properties Matthews coefficient Solvent content 3.45 64.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.594 α = 90 b = 234.985 β = 106.4 c = 106.275 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 PIXEL DECTRIS EIGER X 16M 2019-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03309 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rpim I (All) 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 3.27 43.3 91.9 0.18 0.12 0.952 4.5 2.7 70214 53
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.27 3.38 73.1 0.57 0.43 0.876 1.1 2.2
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 3NSS, 5ITB, 4FQL 3.27 43.3 66845 3351 90.43 0.19841 0.1963 0.1986 0.24078 0.2399 RANDOM 57.757
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] -44.99 -1.54 42.93 2.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.598 r_dihedral_angle_4_deg 15.762 r_dihedral_angle_3_deg 15.586 r_long_range_B_refined 14.546 r_long_range_B_other 14.546 r_mcangle_it 8.599 r_mcangle_other 8.599 r_scangle_other 7.967 r_dihedral_angle_1_deg 6.963 r_mcbond_it 5.476
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.598 r_dihedral_angle_4_deg 15.762 r_dihedral_angle_3_deg 15.586 r_long_range_B_refined 14.546 r_long_range_B_other 14.546 r_mcangle_it 8.599 r_mcangle_other 8.599 r_scangle_other 7.967 r_dihedral_angle_1_deg 6.963 r_mcbond_it 5.476 r_mcbond_other 5.476 r_scbond_it 5.107 r_scbond_other 5.107 r_angle_refined_deg 1.384 r_angle_other_deg 1.342 r_chiral_restr 0.055 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25420 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 121
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing