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Structure of DDB1 bound to CR8-engaged CDK12-cyclinK
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6H0F 6H0F, 4NST experimental model PDB 4NST 6H0F, 4NST
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 292 0.9 M ammonium citrate tribasic
Crystal Properties Matthews coefficient Solvent content 4.11 70.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 250.749 α = 90 b = 250.749 β = 90 c = 217.92 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 EIGER X 16M 2019-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 3.46 54 95.1 0.318 0.092 0.416 7.2 12 89203
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 3.46 3.63 68.3 0.416 0.9 11.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 6H0F, 4NST 3.46 54 89183 4439 86.5 0.1951 0.1938 0.2142 0.22 0.2389 RANDOM 80.62
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] 4.0043 4.0043 -8.0085
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.25 t_omega_torsion 2.87 t_angle_deg 1.01 t_bond_d 0.009 t_dihedral_angle_d t_gen_planes t_it t_nbd t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 33781 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 96
Software Software Software Name Purpose BUSTER refinement DIALS data reduction STARANISO data scaling Aimless data scaling PHASER phasing