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Crystal structure of Z2B3 D102R Fab in complex with influenza virus neuraminidase from A/Serbia/NS-601/2014 (H1N1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BEQ 3BEQ, 5W0D experimental model PDB 5W0D 3BEQ, 5W0D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291.15 0.1M magnesium acetate, 0.1M MES pH 6.5, 10% (w/v) PEG 10000
Crystal Properties Matthews coefficient Solvent content 3.2 61.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 214.442 α = 90 b = 214.442 β = 90 c = 168.68 γ = 120
Symmetry Space Group P 32 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 Nonius Kappa CCD 2019-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97930 SSRF BL17U1
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 3.6 50 100 0.998 6.4 8.3 51355
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 3.6 3.73 0.998
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3BEQ, 5W0D 3.608 25.459 1.33 51355 2511 99.48 0.2164 0.2147 0.2141 0.2488 0.247 97.1993
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.761 f_angle_d 0.634 f_chiral_restr 0.047 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21823 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 164
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing