3LXP

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, and 0.3 M magnesium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9436.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.325α = 90
b = 75.978β = 90
c = 97.415γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDmirror2009-07-07MSINGLE 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
11.6535.499.70.0823.45.5333733337322
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.651.6998.20.541.74.6

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 1YVJ1.6535.43337333373176199.720.193750.191950.22874RANDOM16.044
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]
0.050.06-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.953
r_dihedral_angle_4_deg18.062
r_dihedral_angle_3_deg11.463
r_dihedral_angle_1_deg5.438
r_scangle_it3.222
r_scbond_it2.093
r_mcangle_it1.392
r_angle_refined_deg1.337
r_angle_other_deg1.056
r_mcbond_it0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.953
r_dihedral_angle_4_deg18.062
r_dihedral_angle_3_deg11.463
r_dihedral_angle_1_deg5.438
r_scangle_it3.222
r_scbond_it2.093
r_mcangle_it1.392
r_angle_refined_deg1.337
r_angle_other_deg1.056
r_mcbond_it0.88
r_symmetry_hbond_refined0.228
r_symmetry_vdw_other0.219
r_nbd_refined0.216
r_nbd_other0.185
r_nbtor_refined0.182
r_mcbond_other0.173
r_chiral_restr0.146
r_symmetry_vdw_refined0.13
r_xyhbond_nbd_refined0.122
r_nbtor_other0.083
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
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 Atoms2252
Nucleic Acid Atoms
Solvent Atoms174
Heterogen Atoms23

Software

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