☰ Navigation Tabs
Structure of DDB1 bound to DS17-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 0.9 M ammonium citrate tribasic pH 7.0, NDSB-256 additive
Crystal Properties Matthews coefficient Solvent content 3.93 68.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 249.447 α = 90 b = 249.447 β = 90 c = 218.45 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 2020-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0 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 2.98 216.027 96.6 0.999 16.4 21 139190
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 2.984 3.138 0.401
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-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.98 60.12 1.35 139126 6883 87.63 0.1946 0.1934 0.2181 0.1982 104.35
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 11.8661 f_angle_d 0.7244 f_chiral_restr 0.1098 f_plane_restr 0.0049 f_bond_d 0.0042
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 33736 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 183
Software Software Software Name Purpose PHENIX refinement XDS data reduction Coot model building STARANISO data scaling autoPROC data processing PHASER phasing