2O0U

Crystal structure of human JNK3 complexed with N-{3-cyano-6-[3-(1-piperidinyl)propanoyl]-4,5,6,7-tetrahydrothieno[2,3-c]pyridin-2-yl}-1-naphthalenecarboxamide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.429350mM Tris/HCl, 18-22% PEG3350, 0.2M KF, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4249.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.793α = 90
b = 71.653β = 90
c = 107.857γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42002-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.9326ESRFID14-4

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
122597.20.04921.44.427722
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)
122.0397.10.2814.11374

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.159.662371397196.530.2250.2230.283RANDOM22.363
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]
6.57-2.77-3.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.405
r_dihedral_angle_4_deg22.301
r_dihedral_angle_3_deg18.942
r_dihedral_angle_1_deg6.985
r_scangle_it2.881
r_scbond_it2.084
r_angle_refined_deg1.877
r_mcangle_it1.332
r_mcbond_it1.147
r_angle_other_deg0.993
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.405
r_dihedral_angle_4_deg22.301
r_dihedral_angle_3_deg18.942
r_dihedral_angle_1_deg6.985
r_scangle_it2.881
r_scbond_it2.084
r_angle_refined_deg1.877
r_mcangle_it1.332
r_mcbond_it1.147
r_angle_other_deg0.993
r_symmetry_vdw_other0.28
r_symmetry_hbond_refined0.274
r_symmetry_vdw_refined0.271
r_nbd_refined0.226
r_xyhbond_nbd_refined0.203
r_nbd_other0.201
r_mcbond_other0.199
r_nbtor_refined0.191
r_chiral_restr0.122
r_nbtor_other0.092
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2700
Nucleic Acid Atoms
Solvent Atoms165
Heterogen Atoms34

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction