Evidence: electron density clearly shows the antibody Fab bound to the peptide
Type
Name
Symmetry operation
Number
identity operation
1_555
x,y,z
1
Buried area
4730 Å2
ΔGint
-59 kcal/mol
Surface area
20540 Å2
Unit cell
Length a, b, c (Å)
136.830, 136.830, 116.985
Angle α, β, γ (deg.)
90.000, 90.000, 120.000
Int Tables number
180
Space group name H-M
P6222
-
Components
#1: Antibody
4A3B2-BFabheavychain
Mass: 23862.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi-293 / Production host: Homo sapiens (human)
#2: Antibody
4A3B2-BFablightchain
Mass: 23595.240 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi-293 / Production host: Homo sapiens (human)
#3: Protein/peptide
NeuropeptideY / Neuropeptide tyrosine / NPY
Mass: 4276.728 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01303
Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interest
N
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.93 Å3/Da / Density % sol: 58 % / Description: Rods
Crystal grow
Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Protein complex (~4 mg/mL with respect to Fab, NPY:Fab at molar ratio of 1.4:1, all dissolved in 25 mM Tris (pH 7.5), 100 mM NaCl) was combined to an equal volume (2 uL) of well solution ...Details: Protein complex (~4 mg/mL with respect to Fab, NPY:Fab at molar ratio of 1.4:1, all dissolved in 25 mM Tris (pH 7.5), 100 mM NaCl) was combined to an equal volume (2 uL) of well solution comprising 200 mM Li2SO4, 100 mM sodium acetate (pH 4.5), 22% (w/v) PEG1000
-
Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source
Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
Detector
Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 2, 2019
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Method to determine structure: MOLECULAR REPLACEMENT Starting model: generic Fab Resolution: 2.6→44.79 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.827 / SU B: 23.547 / SU ML: 0.233 / SU R Cruickshank DPI: 0.4227 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.423 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2704
1024
5 %
RANDOM
Rwork
0.2171
-
-
-
obs
0.2198
19349
99.87 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
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