3NYX

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NZ0PDB entry 3NZ0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293PEG3350, sodium acetate, pH 0.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4148.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.318α = 90
b = 70.436β = 90
c = 86.488γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 2102008-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.9774ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.45099.50.137104.41229612234-242

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3NZ02.540122341145068499.530.220.219020.215460.27481RANDOM29.222
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]
1.36-2.030.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.39
r_dihedral_angle_4_deg22.619
r_dihedral_angle_3_deg20.028
r_dihedral_angle_1_deg6.002
r_mcangle_it5.295
r_scangle_it5.13
r_scbond_it3.527
r_mcbond_it3.439
r_angle_refined_deg1.555
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.39
r_dihedral_angle_4_deg22.619
r_dihedral_angle_3_deg20.028
r_dihedral_angle_1_deg6.002
r_mcangle_it5.295
r_scangle_it5.13
r_scbond_it3.527
r_mcbond_it3.439
r_angle_refined_deg1.555
r_nbtor_refined0.309
r_nbd_refined0.21
r_symmetry_vdw_refined0.188
r_xyhbond_nbd_refined0.133
r_symmetry_hbond_refined0.102
r_chiral_restr0.092
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2352
Nucleic Acid Atoms
Solvent Atoms56
Heterogen Atoms41

Software

Software
Software NamePurpose
BOSdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling