5TQ3

Design and Synthesis of a pan-JAK kinase inhibitor clinical candidate (PF-06263276) suitable for the treatment of inflammatory diseases of the lungs and skin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3TJC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1 M Hepes, pH 7.5, 0.1 M Sodium acetate, 30% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.3246.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.854α = 90
b = 182.726β = 110.41
c = 52.766γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2008-05-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G1APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.6940920.1211.92.516600

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3TJC2.6934.541571785890.930.219210.21640.27086RANDOM36.719
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]
-0.660.220.71-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.548
r_dihedral_angle_3_deg18.423
r_dihedral_angle_4_deg18.005
r_dihedral_angle_1_deg10.159
r_long_range_B_other7.246
r_long_range_B_refined7.228
r_scangle_other3.862
r_mcangle_it3.766
r_mcangle_other3.766
r_scbond_other2.394
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.548
r_dihedral_angle_3_deg18.423
r_dihedral_angle_4_deg18.005
r_dihedral_angle_1_deg10.159
r_long_range_B_other7.246
r_long_range_B_refined7.228
r_scangle_other3.862
r_mcangle_it3.766
r_mcangle_other3.766
r_scbond_other2.394
r_scbond_it2.372
r_mcbond_it2.309
r_mcbond_other2.307
r_angle_refined_deg1.571
r_angle_other_deg0.82
r_chiral_restr0.078
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4599
Nucleic Acid Atoms
Solvent Atoms53
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing