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Crystal structure of human CDK8/CYCC in complex with BI-1347
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RGF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 278 32-38% Morpheus Precipitant Mix 4
10 mmol/L Morpheus Buffer System 1
100 mM Morpheus Amino Acids Mix 2% DMSO
Crystal Properties Matthews coefficient Solvent content 2.69 54.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.539 α = 90 b = 73.922 β = 90 c = 168.31 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 EIGER X 16M 2016-08-04 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) 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 2.702 84.2 99.3 12.5 10 24333 69.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.702 2.749
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 3RGF 2.7 37.6 24270 1111 99 0.202 0.201 0.2039 0.231 0.238 RANDOM 56.98
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] 12.0763 -22.3502 10.2739
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.15 t_omega_torsion 2.35 t_angle_deg 0.94 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.15 t_omega_torsion 2.35 t_angle_deg 0.94 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4916 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 27
Software Software Software Name Purpose BUSTER refinement XDS data reduction STARANISO data scaling MOLREP phasing