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Crystal structure of JNK1 in complex with JIP1 peptide and 4-{4-[4-(3-Methanesulfonyl-propoxy)-indazol-1-yl]-pyrimidin-2-ylamino}-cyclohexan
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UKH PDB ENTRY 1UKH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 289 20% PEG 3350, 0.2 M LiSO4, 0.1 M BIS-TRIS, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.32 46.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.438 α = 90 b = 81.769 β = 90 c = 82.502 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 CCD ADSC QUANTUM 315r M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.15 58.12 95.4 0.099 16.6 6.4 21746
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.23 71.3 0.447 1.74 3.4 1592
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-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1UKH 2.152 58.12 20592 1109 95.22 0.23122 0.2292 0.26898 0.2729 RANDOM 48.425
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] -2.02 3.12 -1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.633 r_dihedral_angle_3_deg 16.151 r_dihedral_angle_4_deg 14.178 r_dihedral_angle_1_deg 5.834 r_scangle_it 2.126 r_scbond_it 1.322 r_angle_refined_deg 1.126 r_mcangle_it 1.019 r_mcbond_it 0.592 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.633 r_dihedral_angle_3_deg 16.151 r_dihedral_angle_4_deg 14.178 r_dihedral_angle_1_deg 5.834 r_scangle_it 2.126 r_scbond_it 1.322 r_angle_refined_deg 1.126 r_mcangle_it 1.019 r_mcbond_it 0.592 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.269 r_symmetry_hbond_refined 0.196 r_nbd_refined 0.191 r_xyhbond_nbd_refined 0.129 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2674 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 31
Software Software Software Name Purpose ADSC data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing