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Crystal structure of the RSV F glycoprotein in complex with the neutralizing single-domain antibody F-VHH-L66
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MMS Prefusion F (PDB entry 4MMS) and unbound F-VHH-4 structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 293 4.79 mg/mL EndoH-digested DS-Cav1 + F-VHH-L66, 0.05 M potassium phosphate, 20% w/v PEG4000
Crystal Properties Matthews coefficient Solvent content 2.73 54.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.89 α = 90 b = 138.89 β = 90 c = 221.902 γ = 120
Symmetry Space Group P 31 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 ADSC QUANTUM 315r 2015-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97934 APS 19-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 3.8 50.38 99.9 0.332 0.368 0.157 0.975 5.2 5.3 25035 95.53
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 3.8 4.06 100 1.246 1.378 0.581 0.549 5.5 4457
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 FREE R-VALUE Prefusion F (PDB entry 4MMS) and unbound F-VHH-4 structure 3.8 50.376 1.34 24981 1205 99.9 0.2494 0.2475 0.2549 0.2858 0.286 124.023
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 12.509 f_angle_d 1.127 f_chiral_restr 0.048 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13952 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 47
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing