3NZ0 | pdb_00003nz0

Non-phosphorylated TYK2 kinase with CMP6


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2B7APDB entry 2B7A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293KSCN, PEG3350, hexafluoro-2-propanol, pH 0.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1843.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.59α = 90
b = 64.91β = 90
c = 83.02γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATERIGAKU RAXIS IV++2007-09-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54

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
11.93098.40.085115.42475024354-222

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2B7A228.32011020105109699.630.2120.211020.208790.210.253470.26RANDOM21.401
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]
0.1-0.06-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.703
r_dihedral_angle_4_deg20.71
r_dihedral_angle_3_deg13.678
r_dihedral_angle_1_deg5.625
r_scangle_it3.279
r_mcangle_it3.183
r_mcbond_it2.866
r_scbond_it2.376
r_angle_refined_deg1.285
r_angle_other_deg0.879
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.703
r_dihedral_angle_4_deg20.71
r_dihedral_angle_3_deg13.678
r_dihedral_angle_1_deg5.625
r_scangle_it3.279
r_mcangle_it3.183
r_mcbond_it2.866
r_scbond_it2.376
r_angle_refined_deg1.285
r_angle_other_deg0.879
r_mcbond_other0.341
r_symmetry_vdw_other0.241
r_symmetry_hbond_refined0.209
r_nbd_refined0.195
r_symmetry_vdw_refined0.193
r_nbd_other0.186
r_nbtor_refined0.176
r_xyhbond_nbd_refined0.131
r_nbtor_other0.079
r_chiral_restr0.071
r_bond_refined_d0.007
r_bond_other_d0.007
r_gen_planes_refined0.003
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2331
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms23

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling