6DF3 | pdb_00006df3

Crystal structure of ternary complex of IL-24 with soluble receptors IL-22RA and IL-20RB

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4DOH	PDB entry 4DOH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	8 mg/mL protein in 0.2 M sodium chloride, 0.05 M HEPES against 215 w/v MEPEG2000, 0.05 M Tris, pH 8.5, 0.05 M trimethylamine N-oxide dihydrate

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.702	α = 90
b = 77.702	β = 90
c = 124.785	γ = 90

Symmetry
Space Group	P 43

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	MARMOSAIC 300 mm CCD		2017-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.00000	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.15	99	99.7	0.072	0.034	0.97	29.7	8		39903

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.23	100		1.416	0.62	0.7	1.62	7.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 4DOH	2.15	30	37897	1978	99.7	0.1838	0.1816	0.2246	0.2423	RANDOM	74.672

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]
1.75			1.75		-3.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.478
r_dihedral_angle_4_deg	18.073
r_dihedral_angle_3_deg	17.224
r_dihedral_angle_1_deg	7.899
r_angle_refined_deg	2.018
r_angle_other_deg	1.08
r_chiral_restr	0.117
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4395
Nucleic Acid Atoms
Solvent Atoms	80
Heterogen Atoms	54

Software

Software
Software Name	Purpose
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction