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Crystal structure of JNK3 in complex with a pyridinylimidazole inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4X21
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100 mM Bis-Tris pH5.5, 200 mM NaCl, 29% PEG 3350, 1mM AMP-PCP, 0.4 mM Zwittergent 3-14, 10% Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.36 47.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.56 α = 90 b = 114.26 β = 90 c = 157.8 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M-F 2017-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.9 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.76 50 99.9 0.089 22.98 26.4 157963
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4X21 1.76 48.01 156383 99.9 0.261
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] -0.48 0.88 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.127 r_dihedral_angle_4_deg 20.771 r_dihedral_angle_3_deg 14.423 r_dihedral_angle_1_deg 6.559 r_long_range_B_refined 6.031 r_long_range_B_other 6.031 r_scangle_other 1.667 r_angle_refined_deg 1.515 r_mcangle_it 1.393 r_mcangle_other 1.393
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.127 r_dihedral_angle_4_deg 20.771 r_dihedral_angle_3_deg 14.423 r_dihedral_angle_1_deg 6.559 r_long_range_B_refined 6.031 r_long_range_B_other 6.031 r_scangle_other 1.667 r_angle_refined_deg 1.515 r_mcangle_it 1.393 r_mcangle_other 1.393 r_scbond_it 1.165 r_scbond_other 1.165 r_angle_other_deg 0.937 r_mcbond_it 0.848 r_mcbond_other 0.848 r_chiral_restr 0.131 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 10762 Nucleic Acid Atoms Solvent Atoms 861 Heterogen Atoms 211
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing