3NYX | pdb_00003nyx

Non-phosphorylated TYK2 JH1 domain with Quinoline-Thiadiazole-Thiophene Inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NZ0	PDB entry 3NZ0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	PEG3350, sodium acetate, pH 0.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.318	α = 90
b = 70.436	β = 90
c = 86.488	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	ADSC QUANTUM 210		2008-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.9774	ALS	5.0.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	2.4	50	99.5	0.137	10	4.4	12296	12234		-2	42

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	PDB entry 3NZ0	2.5	40	12234	11450	684	99.53	0.22	0.21902	0.21546	0.22	0.27481	0.27	RANDOM	29.222

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]
1.36			-2.03		0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.39
r_dihedral_angle_4_deg	22.619
r_dihedral_angle_3_deg	20.028
r_dihedral_angle_1_deg	6.002
r_mcangle_it	5.295
r_scangle_it	5.13
r_scbond_it	3.527
r_mcbond_it	3.439
r_angle_refined_deg	1.555
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.39
r_dihedral_angle_4_deg	22.619
r_dihedral_angle_3_deg	20.028
r_dihedral_angle_1_deg	6.002
r_mcangle_it	5.295
r_scangle_it	5.13
r_scbond_it	3.527
r_mcbond_it	3.439
r_angle_refined_deg	1.555
r_nbtor_refined	0.309
r_nbd_refined	0.21
r_symmetry_vdw_refined	0.188
r_xyhbond_nbd_refined	0.133
r_symmetry_hbond_refined	0.102
r_chiral_restr	0.092
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2352
Nucleic Acid Atoms
Solvent Atoms	56
Heterogen Atoms	41

Software

Software
Software Name	Purpose
BOS	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.