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The Crystal Structure of human JNK2 from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NPC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M Na/K PO4, 20% PEG3,350
Crystal Properties Matthews coefficient Solvent content 2.18 43.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.004 α = 90 b = 102.004 β = 90 c = 70.088 γ = 90
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 PILATUS3 6M 2020-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
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 2.15 19.616 99.8 0.141 10.8 9.1 39267
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 2.15 2.22 1.269
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3npc 2.15 19.616 39264 1929 99.794 0.286 0.2842 0.2928 0.3274 0.3331 36.292
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] 0.703 0.703 -1.406
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.273 r_dihedral_angle_4_deg 17.112 r_dihedral_angle_3_deg 16.065 r_dihedral_angle_1_deg 6.748 r_lrange_it 5.027 r_lrange_other 5.024 r_mcangle_it 2.982 r_mcangle_other 2.981 r_scangle_it 2.928 r_scangle_other 2.927
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.273 r_dihedral_angle_4_deg 17.112 r_dihedral_angle_3_deg 16.065 r_dihedral_angle_1_deg 6.748 r_lrange_it 5.027 r_lrange_other 5.024 r_mcangle_it 2.982 r_mcangle_other 2.981 r_scangle_it 2.928 r_scangle_other 2.927 r_mcbond_it 1.747 r_mcbond_other 1.746 r_scbond_it 1.693 r_scbond_other 1.692 r_angle_refined_deg 1.227 r_angle_other_deg 1.112 r_nbd_refined 0.189 r_nbd_other 0.181 r_symmetry_nbd_other 0.173 r_symmetry_nbd_refined 0.173 r_nbtor_refined 0.155 r_xyhbond_nbd_refined 0.149 r_symmetry_xyhbond_nbd_refined 0.143 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.053 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5406 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing