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CDK8-CYCC IN COMPLEX WITH 8-(1-Methyl-2,2-dioxo-2,3-dihydro-1H-2l6-benzo[c]isothiazol-5-yl)-[1,6]naphthyridine-2-carboxylic acid methylamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4F6S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 293 20% PEG3350, 0.2 M sodium formate, pH 6.9
Crystal Properties Matthews coefficient Solvent content 3.1 59.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.749 α = 90 b = 71.282 β = 90 c = 171.953 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 DECTRIS PILATUS 6M 2012-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00000 SLS X06SA
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 2.6 85.98 97.2 0.08 17.7 4.1 27530
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 2.6 2.85 97.2 0.503 3.9
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 FOURIER SYNTHESIS THROUGHOUT 4f6s 2.6 85.98 25840 926 97.23 0.23873 0.23741 0.2466 0.27423 0.2777 RANDOM 42.716
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] -1.13 -0.57 1.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.638 r_dihedral_angle_4_deg 18.286 r_dihedral_angle_3_deg 13.768 r_dihedral_angle_1_deg 6.06 r_scangle_it 4.332 r_scbond_it 3.071 r_mcangle_it 2.089 r_mcbond_it 1.655 r_angle_refined_deg 1.224 r_angle_other_deg 0.933
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.638 r_dihedral_angle_4_deg 18.286 r_dihedral_angle_3_deg 13.768 r_dihedral_angle_1_deg 6.06 r_scangle_it 4.332 r_scbond_it 3.071 r_mcangle_it 2.089 r_mcbond_it 1.655 r_angle_refined_deg 1.224 r_angle_other_deg 0.933 r_mcbond_other 0.299 r_nbd_refined 0.18 r_nbtor_refined 0.166 r_symmetry_vdw_other 0.154 r_nbd_other 0.134 r_xyhbond_nbd_refined 0.103 r_symmetry_vdw_refined 0.084 r_symmetry_hbond_refined 0.08 r_nbtor_other 0.074 r_chiral_restr 0.072 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5064 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 32
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement