6GLA

Crystal structure of JAK3 in complex with Compound 11 (FM481)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5LWM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277.1524-30% PEG 3350, 0.1 M MES, pH 5.5-6.0 and 0.1-0.2 M MgCl2
Crystal Properties
Matthews coefficientSolvent content
1.9336.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.951α = 90
b = 61.358β = 92.37
c = 100.434γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-05-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

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
11.9252.3599.90.1464.94.139077
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.922.0299.50.52824

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 REPLACEMENTTHROUGHOUT5lwm1.9252.3537123192899.880.228390.225990.27339RANDOM26.804
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]
-3.040.250.022.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.224
r_dihedral_angle_4_deg16.848
r_dihedral_angle_3_deg13.323
r_dihedral_angle_1_deg6.267
r_long_range_B_refined4.917
r_long_range_B_other4.917
r_scangle_other2.431
r_mcangle_it2.095
r_mcangle_other2.095
r_angle_refined_deg1.662
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.224
r_dihedral_angle_4_deg16.848
r_dihedral_angle_3_deg13.323
r_dihedral_angle_1_deg6.267
r_long_range_B_refined4.917
r_long_range_B_other4.917
r_scangle_other2.431
r_mcangle_it2.095
r_mcangle_other2.095
r_angle_refined_deg1.662
r_scbond_it1.476
r_scbond_other1.476
r_mcbond_it1.233
r_mcbond_other1.233
r_angle_other_deg1.226
r_chiral_restr0.1
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.006
r_gen_planes_other0.004
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 Atoms4566
Nucleic Acid Atoms
Solvent Atoms233
Heterogen Atoms106

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing