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Crystal structure of human CDK8/CYCC in complex with compound 11 (1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-(5-hydroxypentyl)urea)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RGF PDB ENTRY 3RGF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 293.15 20% PEG3350, 0.2 M sodium formate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.89 57.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.157 α = 90 b = 71.76 β = 90 c = 180.362 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 2012-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00001 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 2.65 90.19 99.7 0.076 8.5 3.7 27863 27863
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 2.65 2.86 99.6 0.515 1.4 3.7
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 (All) 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 3RGF 2.65 90.19 27863 26899 908 99.63 0.19986 0.19986 0.19893 0.2086 0.22794 0.2363 RANDOM 59.491
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] 1.43 -1.78 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.138 r_dihedral_angle_4_deg 15.202 r_dihedral_angle_3_deg 12.227 r_dihedral_angle_1_deg 5.29 r_scangle_it 3.803 r_scbond_it 2.607 r_mcangle_it 1.741 r_mcbond_it 1.418 r_angle_refined_deg 1.178 r_angle_other_deg 0.931
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.138 r_dihedral_angle_4_deg 15.202 r_dihedral_angle_3_deg 12.227 r_dihedral_angle_1_deg 5.29 r_scangle_it 3.803 r_scbond_it 2.607 r_mcangle_it 1.741 r_mcbond_it 1.418 r_angle_refined_deg 1.178 r_angle_other_deg 0.931 r_mcbond_other 0.212 r_nbd_refined 0.171 r_nbtor_refined 0.162 r_symmetry_vdw_other 0.133 r_nbd_other 0.132 r_symmetry_hbond_refined 0.129 r_xyhbond_nbd_refined 0.108 r_symmetry_vdw_refined 0.083 r_nbtor_other 0.075 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4993 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 34
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling