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Structure of the Porcine Reproductive and Respiratory Syndrome virus-2 glycoprotein GP4 antigenic region 59-69 bound to the neutralizing scFv#18
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KVD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 20 % w/v Polyethylene glycol monomethyl ether 5,000, 200 mM lithium acetate
Crystal Properties Matthews coefficient Solvent content 3.59 65.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.283 α = 90 b = 108.849 β = 90 c = 50.156 γ = 90
Symmetry Space Group P 21 21 2
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 2024-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.978565 SOLEIL PROXIMA 1
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 2.3 50 100 0.997 8.22 13.3 18229
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 2.3 2.44 0.75
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.3 45.55 14639 729 80.3 0.2036 0.2014 0.1946 0.2459 0.2483 RANDOM 40.21
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] -1.9742 -6.2963 8.2705
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.22 t_omega_torsion 3.27 t_angle_deg 0.97 t_bond_d 0.007 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1926 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 17
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing