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Structure of DDB1 bound to DS06-engaged CDK12-cyclin K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TD3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.38 M ammonium sulphate, 0.07 M HEPES, pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.93 68.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 249.353 α = 90 b = 249.353 β = 90 c = 218.417 γ = 120
Symmetry Space Group P 31 2 1
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 EIGER2 X 16M 2020-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99995 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 3.618 215.946 95.8 0.99 11.6 21.1 81004
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.618 3.784 0.41
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.62 76.78 1.34 80955 4039 90.47 0.164 0.1795 0.2059 0.2175 158.71
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.7393 f_angle_d 0.8502 f_chiral_restr 0.0508 f_plane_restr 0.0056 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 33696 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 151
Software Software Software Name Purpose PHENIX refinement XDS data reduction Coot model building STARANISO data scaling autoPROC data processing PHASER phasing