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Crystal structure of CDK12/Cyclin K in complex with covalent inhibitor ZLC853
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9JK1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.02 M of each monosaccharide, 0.1 M MES/imidazole pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.72 54.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.12 α = 90 b = 114.12 β = 90 c = 103.06 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 PILATUS3 6M 2024-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NFPSS BEAMLINE BL18U 0.97946 NFPSS BL18U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.2 37.353 99.9 0.123 0.999 17.2 18.8 13154
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 3.2 3.42 100 0.908
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3.28 37.35 12214 630 99.837 0.2 0.1971 0.1985 0.2471 0.2465 RANDOM 131.09
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] 3.216 1.608 3.216 -10.433
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 29.491 r_scangle_it 25.286 r_mcangle_it 22.407 r_scbond_it 18.164 r_dihedral_angle_3_deg 18.07 r_mcbond_it 15.557 r_dihedral_angle_6_deg 15.469 r_dihedral_angle_2_deg 7.177 r_dihedral_angle_1_deg 5.245 r_angle_refined_deg 1.567
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 29.491 r_scangle_it 25.286 r_mcangle_it 22.407 r_scbond_it 18.164 r_dihedral_angle_3_deg 18.07 r_mcbond_it 15.557 r_dihedral_angle_6_deg 15.469 r_dihedral_angle_2_deg 7.177 r_dihedral_angle_1_deg 5.245 r_angle_refined_deg 1.567 r_nbtor_refined 0.313 r_nbd_refined 0.201 r_symmetry_nbd_refined 0.198 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.113 r_symmetry_xyhbond_nbd_refined 0.02 r_bond_refined_d 0.007 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4410 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction gemmi data extraction PHASER phasing