☰ Navigation Tabs
Crystal structure of human CDK8/CYCC in complex with compound 3 (1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-(2-hydroxyethyl)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 2.82 56.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.529 α = 90 b = 71.908 β = 90 c = 176.897 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 1.00002 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 88.45 99.7 0.09 7.2 5.4 28771 28771
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 2.81 99.4 0.504 1.5 5.5
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 2.6 88.45 28771 27752 958 99.52 0.22933 0.22933 0.2277 0.2292 0.27648 0.28 RANDOM 46.749
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] 1.37 -4.42 3.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.167 r_dihedral_angle_3_deg 15.031 r_dihedral_angle_4_deg 12.386 r_scangle_it 6.027 r_dihedral_angle_1_deg 5.88 r_scbond_it 4.061 r_mcangle_it 2.887 r_mcbond_it 1.619 r_angle_refined_deg 1.23 r_angle_other_deg 1.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.167 r_dihedral_angle_3_deg 15.031 r_dihedral_angle_4_deg 12.386 r_scangle_it 6.027 r_dihedral_angle_1_deg 5.88 r_scbond_it 4.061 r_mcangle_it 2.887 r_mcbond_it 1.619 r_angle_refined_deg 1.23 r_angle_other_deg 1.013 r_mcbond_other 0.322 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4934 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 30
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling