3LXL

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 DROP7.529320% PEG-3350, 0.2 M Ammonium Sulfate, 0.02% phenylurea, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1242.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.192α = 90
b = 75.187β = 90
c = 89.07γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDMARMOSAIC 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
11.7425.131000.0347.96.93142222
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)
1.741.81000.330.333.566.7

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 1YVJ1.7425.133142231422167899.580.1950.19330.22697RANDOM21.427
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]
0.06-0.01-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.287
r_dihedral_angle_4_deg20.748
r_dihedral_angle_3_deg12.714
r_dihedral_angle_1_deg8.24
r_scangle_it2.869
r_scbond_it1.832
r_angle_refined_deg1.364
r_mcangle_it1.34
r_angle_other_deg0.986
r_mcbond_it0.893
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.287
r_dihedral_angle_4_deg20.748
r_dihedral_angle_3_deg12.714
r_dihedral_angle_1_deg8.24
r_scangle_it2.869
r_scbond_it1.832
r_angle_refined_deg1.364
r_mcangle_it1.34
r_angle_other_deg0.986
r_mcbond_it0.893
r_symmetry_vdw_other0.343
r_nbd_refined0.226
r_chiral_restr0.204
r_nbd_other0.196
r_symmetry_vdw_refined0.193
r_nbtor_refined0.182
r_mcbond_other0.181
r_xyhbond_nbd_refined0.137
r_symmetry_hbond_refined0.117
r_nbtor_other0.084
r_bond_refined_d0.01
r_gen_planes_refined0.005
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 Atoms2217
Nucleic Acid Atoms
Solvent Atoms289
Heterogen Atoms23

Software

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