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Crystal structure of human CDK8/CYCC in complex with compound 5 (1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-[3-(morpholin-4-yl)propyl]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 2.69 54.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.397 α = 90 b = 71.024 β = 90 c = 171.217 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 2011-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.99987 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 2.1 85.61 99.9 0.065 8.1 51652 51652
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 2.1 2.27 100 0.549 8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3RGF 2.1 85.61 51626 49911 1715 99.95 0.1772 0.1772 0.17649 0.19756 0.216 RANDOM 45.108
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] -0.86 0.36 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.185 r_dihedral_angle_4_deg 13.861 r_dihedral_angle_3_deg 11.838 r_dihedral_angle_1_deg 5.509 r_scangle_it 5.509 r_scbond_it 3.774 r_mcangle_it 2.687 r_mcbond_it 1.569 r_angle_refined_deg 1.21 r_angle_other_deg 1.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.185 r_dihedral_angle_4_deg 13.861 r_dihedral_angle_3_deg 11.838 r_dihedral_angle_1_deg 5.509 r_scangle_it 5.509 r_scbond_it 3.774 r_mcangle_it 2.687 r_mcbond_it 1.569 r_angle_refined_deg 1.21 r_angle_other_deg 1.019 r_mcbond_other 0.453 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4986 Nucleic Acid Atoms Solvent Atoms 309 Heterogen Atoms 92
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling