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Structure of human JNK1 in complex with SCH772984 and the AMPPNP-hydrolysed triphosphate revealing the second type-I binding mode
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YDI pdb entry 2YDI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 12-15% PEG3350 and 0.1 M HEPES pH 6.8-7.8, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties Matthews coefficient Solvent content 2.34 47.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.95 α = 90 b = 71.55 β = 90 c = 108.17 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 PSI PILATUS 6M Kirkpatrick Baez bimorph mirror pair 2014-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97625 Diamond I04
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 1.5 25.75 99.9 0.064 14.9 6.4 64041 63969 15.2
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 1.5 1.58 99.4 0.497 3.1 4.9 9131
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 2YDI 1.5 59.68 2 63969 60781 3187 99.85 0.16692 0.1656 0.1658 0.19211 0.1919 RANDOM 24.467
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 -0.14 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.269 r_dihedral_angle_4_deg 18.88 r_dihedral_angle_3_deg 13.564 r_long_range_B_refined 6.992 r_long_range_B_other 6.991 r_dihedral_angle_1_deg 6.085 r_scangle_other 3.548 r_scbond_it 2.483 r_scbond_other 2.481 r_mcangle_other 2.243
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.269 r_dihedral_angle_4_deg 18.88 r_dihedral_angle_3_deg 13.564 r_long_range_B_refined 6.992 r_long_range_B_other 6.991 r_dihedral_angle_1_deg 6.085 r_scangle_other 3.548 r_scbond_it 2.483 r_scbond_other 2.481 r_mcangle_other 2.243 r_mcangle_it 2.242 r_angle_refined_deg 1.613 r_mcbond_other 1.415 r_mcbond_it 1.414 r_angle_other_deg 0.802 r_chiral_restr 0.104 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2871 Nucleic Acid Atoms Solvent Atoms 367 Heterogen Atoms 161
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling