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JNK3 bound to aminopyrimidine inhibitor, SR-3562
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FI3 PDB entry 3FI3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5.5 293 10MG/ML JNK3 MIXED WITH 1MM AMP-PCP, 2MM MGCL2, 0.4MM ZWITTERGENT 3-14, AND 10% ETHYLENE GLYCOL. CRYSTALS GROWN IN 0.2M NACL, 0.1M BIS-TRIS, 28-31% PEG 3350, PH 5.5. Ligand soaked in to crystals., microbatch, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.08 40.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.362 α = 90 b = 125.642 β = 90 c = 68.744 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 315 2007-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 1.0 SSRL BL9-1
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 2.4 68.29 98.6 0.062 3.7 13329 2 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB entry 3FI3 2.4 23.38 13329 13142 708 98.6 0.22205 0.21957 0.2274 0.26933 0.2847 RANDOM 31.973
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] -2.81 1.02 1.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.783 r_dihedral_angle_4_deg 23.342 r_dihedral_angle_3_deg 17.682 r_dihedral_angle_1_deg 6.884 r_scangle_it 4.788 r_scbond_it 3.347 r_mcangle_it 2.134 r_angle_refined_deg 2.107 r_mcbond_it 1.21 r_chiral_restr 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.783 r_dihedral_angle_4_deg 23.342 r_dihedral_angle_3_deg 17.682 r_dihedral_angle_1_deg 6.884 r_scangle_it 4.788 r_scbond_it 3.347 r_mcangle_it 2.134 r_angle_refined_deg 2.107 r_mcbond_it 1.21 r_chiral_restr 0.127 r_gen_planes_refined 0.022 r_bond_refined_d 0.021 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2531 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 37
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling