9EZA | pdb_00009eza

Interleukin-31 Receptor D1D2 in complex with Nemolizumab derived scFv

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5F3H	scFV fragment

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		287	MorpheusII H6 (40 mM Polyamines, 10% PEG4000, 20% 1,2,6-Hexanetriol, 100 mM BES pH 7)

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.008	α = 90
b = 163.559	β = 90
c = 269.466	γ = 90

Symmetry
Space Group	C 2 2 21

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		2019-01-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.9786	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.147	78.378	99.8	0.112	0.998	10.26	6.73		70477			56.558

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.147	2.28	98.9		1.881	0.302	0.71	5.98

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.147	46.745	70223	1995	99.541	0.202	0.2009	0.2005	0.2303	0.2309	66.578

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]
0.284			0.197		-0.482

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.236
r_dihedral_angle_6_deg	12.49
r_lrange_it	7.801
r_lrange_other	7.801
r_dihedral_angle_1_deg	7.549
r_scangle_it	5.786
r_scangle_other	5.786
r_dihedral_angle_2_deg	5.589
r_mcangle_it	4.067
r_mcangle_other	4.067
r_scbond_it	3.745
r_scbond_other	3.745
r_mcbond_it	2.713
r_mcbond_other	2.713
r_angle_refined_deg	1.488
r_angle_other_deg	0.517
r_nbd_refined	0.196
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.182
r_nbd_other	0.158
r_xyhbond_nbd_refined	0.146
r_symmetry_nbd_refined	0.143
r_symmetry_xyhbond_nbd_refined	0.097
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.067
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6901
Nucleic Acid Atoms
Solvent Atoms	242
Heterogen Atoms	69

Software

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