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The Crystal Structure of JNK from Drosophila melanogaster Reveals an Evolutionarily Conserved Topology with that of Mammalian JNK Proteins.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XS0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 25% (w/v) PEG 4000, 0.1 M Tris-HCl pH 8.5 and 0.2 M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.02 39.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.486 α = 90 b = 55.329 β = 90 c = 126.717 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 RAYONIX MX225HE 2012-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.58 28.28 99.4 0.062 0.118 4.3 51133 20.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.58 1.66 97.6 0.794 1.8 4.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2XS0 1.79 28.28 31789 3586 99.33 0.17936 0.17474 0.1881 0.21956 0.2231 RANDOM 26.457
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.087 r_dihedral_angle_4_deg 14.422 r_dihedral_angle_3_deg 13.719 r_long_range_B_refined 7.322 r_long_range_B_other 7.274 r_dihedral_angle_1_deg 6.086 r_scangle_other 5.731 r_mcangle_it 3.901 r_mcangle_other 3.899 r_scbond_other 3.796
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.087 r_dihedral_angle_4_deg 14.422 r_dihedral_angle_3_deg 13.719 r_long_range_B_refined 7.322 r_long_range_B_other 7.274 r_dihedral_angle_1_deg 6.086 r_scangle_other 5.731 r_mcangle_it 3.901 r_mcangle_other 3.899 r_scbond_other 3.796 r_scbond_it 3.795 r_mcbond_it 2.71 r_mcbond_other 2.703 r_angle_refined_deg 1.982 r_angle_other_deg 1.115 r_chiral_restr 0.128 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 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 2810 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction HKL-2000 data scaling MOLREP phasing