3LXN

Structural and Thermodynamic Characterization of the TYK2 and JAK3 Kinase Domains in Complex with CP-690550 and CMP-6


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YVJPDB entry 1YVJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829310% Ethanol, 0.1 M Tris, 0.3 M magnesium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9637.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.306α = 90
b = 74.262β = 90
c = 106.46γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDmirrors2009-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.5418APS21-ID-D

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
12.518.699.70.06831.876100021000222
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.52.561000.1020.196.3

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1YVJ2.518.58100021000250299.60.22330.220210.28637RANDOM15.63
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]
0.19-0.15-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.183
r_dihedral_angle_4_deg20.479
r_dihedral_angle_3_deg18.891
r_dihedral_angle_1_deg9.547
r_scangle_it1.87
r_angle_refined_deg1.405
r_angle_other_deg1.3
r_scbond_it1.189
r_mcangle_it1.081
r_mcbond_it0.626
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.183
r_dihedral_angle_4_deg20.479
r_dihedral_angle_3_deg18.891
r_dihedral_angle_1_deg9.547
r_scangle_it1.87
r_angle_refined_deg1.405
r_angle_other_deg1.3
r_scbond_it1.189
r_mcangle_it1.081
r_mcbond_it0.626
r_symmetry_vdw_other0.22
r_nbd_refined0.208
r_nbd_other0.193
r_nbtor_refined0.192
r_symmetry_hbond_refined0.187
r_chiral_restr0.171
r_xyhbond_nbd_refined0.146
r_symmetry_vdw_refined0.117
r_nbtor_other0.09
r_mcbond_other0.085
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.002
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 Atoms2238
Nucleic Acid Atoms
Solvent Atoms88
Heterogen Atoms23

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling