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Crystal Structure of the Computationally Designed Influenza Hemagglutinin Epitope Scaffold stem_mimetic_01 bound by Antibody CR9501
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FQH experimental model PDB 1YA9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Ammonium citrate dibasic, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.38 48.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 269.004 α = 90 b = 55.943 β = 90.597 c = 92.01 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 EIGER X 16M 2020-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.711 37.79 90.71 0.14 0.168 0.089 0.814 13.38 3.5 36153 45.95
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.711 2.808 0.678 0.7936 0.4058 0.651 2.9
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4FQH, 1YA9 2.711 37.79 1.36 34211 2680 62.36 0.1985 0.1986 0.2025 0.246 0.2485 random selection 44.82
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 20.384 f_angle_d 0.5411 f_chiral_restr 0.0419 f_plane_restr 0.0041 f_bond_d 0.0026
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8684 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms
Software Software Software Name Purpose SERGUI data collection PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing