Experiment: 8K4Q

Crystal structure of nanobody HuNb103 bound to human interleukin-4 receptor subunit alpha

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	Reservoir condition: 0.1M HEPES pH 7.0, 20% PEG8000. Sample buffer: 25mM HEPES pH 7.49, 150mM NaCl. Cryoprotectant condition: 0.1M HEPES pH 7.0, 20% PEG8000, 15% ethylene glycol.

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.87	α = 90
b = 109.598	β = 98.48
c = 64.167	γ = 90

Symmetry
Space Group	P 1 21 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 EIGER2 S 9M		2023-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.97918	SSRF	BL02U1

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	2.59	109.6	100	0.155	0.169	0.066	0.994	9.7	6.5		24709

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	2.59	2.66		100	2.158	2.351	0.925	0.412		6.4

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	2.59	57.3	23495	1186	99.96	0.2249	0.22211	0.2612	0.27987	0.3048	RANDOM	31.526

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]
1.54		1.35	-4.38		2.33

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4981
Nucleic Acid Atoms
Solvent Atoms	137
Heterogen Atoms	190

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data scaling
DIALS	data reduction
PHASER	phasing