6EKD

Crystal structure of JNK3 in complex with a pyridinylimidazole inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4X21 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293100 mM Bis Tris pH 5.5, 200 mM NaCl, 29% PEG 3350, 1 mM AMP-PCP, 0.4 mM Zwittergent 3-14, 10% Ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
2.0740.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.51α = 90
b = 124.82β = 90
c = 68.89γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2017-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.0SLSX06DA

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
12.1501000.13226.425.820913
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)
12.12.152.982

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 REPLACEMENTTHROUGHOUT4X212.148.4819867104699.980.208170.20560.25902RANDOM52.355
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]
-0.68-0.10.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.301
r_dihedral_angle_4_deg23.647
r_dihedral_angle_3_deg15.145
r_dihedral_angle_1_deg7.018
r_long_range_B_refined4.485
r_long_range_B_other4.484
r_scangle_other1.764
r_mcangle_it1.726
r_mcangle_other1.725
r_angle_refined_deg1.513
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.301
r_dihedral_angle_4_deg23.647
r_dihedral_angle_3_deg15.145
r_dihedral_angle_1_deg7.018
r_long_range_B_refined4.485
r_long_range_B_other4.484
r_scangle_other1.764
r_mcangle_it1.726
r_mcangle_other1.725
r_angle_refined_deg1.513
r_scbond_it1.24
r_scbond_other1.236
r_mcbond_it1.046
r_mcbond_other1.046
r_angle_other_deg0.98
r_chiral_restr0.095
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms2539
Nucleic Acid Atoms
Solvent Atoms104
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing