5TOJ

Crystal structure of the RSV F glycoprotein in complex with the neutralizing single-domain antibody F-VHH-4


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4MMSPrefusion F (PDB entry 4MMS) and unbound F-VHH-4 structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52932.45 mg/mL EndoH-digested DS-Cav1 + F-VHH-4, 14.75% w/v PEG3350, 8.8% v/v isopropanol, 0.2 M ammonium citrate
Crystal Properties
Matthews coefficientSolvent content
2.9358.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 173.189α = 90
b = 173.189β = 90
c = 153.301γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2015-08-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.03320APS23-ID-B

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.337.9699.90.1880.2020.0730.9959.27.44031185.08
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)RedundancyNumber Unique Reflections (All)
13.33.431001.0811.1590.4150.5457.54477

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEPrefusion F (PDB entry 4MMS) and unbound F-VHH-4 structure3.337.9561.3540277202299.990.18660.18410.234394.5094
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.375
f_angle_d1.195
f_chiral_restr0.048
f_bond_d0.005
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14082
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms42

Software

Software
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing