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CDK8-CYCC IN COMPLEX WITH [6-Hydroxy-3-(3-methyl-benzyl)-1H-indazol-5-yl]-((S)-3-hydroxy-pyrrolidin-1-yl)-methanone
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 293 20% PEG3350, 0.2M lithium chloride
Crystal Properties Matthews coefficient Solvent content 3.08 60.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.232 α = 90 b = 71.439 β = 90 c = 171 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 2013-12-01 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 2.35 85.5 99.7 0.104 15.1 7.7 37088
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 2.35 2.6 99.2 0.544 7.8
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 2.35 85.5 35866 1222 99.74 0.2183 0.21712 0.2249 0.25243 0.2601 RANDOM 48.06
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] 0.32 0.21 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.164 r_dihedral_angle_4_deg 12.739 r_dihedral_angle_3_deg 11.53 r_dihedral_angle_1_deg 5.28 r_scangle_it 4.595 r_scbond_it 3.034 r_mcangle_it 2.224 r_mcbond_it 1.21 r_angle_refined_deg 1.11 r_angle_other_deg 0.996
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.164 r_dihedral_angle_4_deg 12.739 r_dihedral_angle_3_deg 11.53 r_dihedral_angle_1_deg 5.28 r_scangle_it 4.595 r_scbond_it 3.034 r_mcangle_it 2.224 r_mcbond_it 1.21 r_angle_refined_deg 1.11 r_angle_other_deg 0.996 r_mcbond_other 0.243 r_chiral_restr 0.063 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_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 5040 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 52
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement