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Crystal Structure of Human CDK9/cyclinT1 with A86
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BLH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 277.15 CDK9/Cyclin T1 at a concentration of 4.5 mg/ml (20 mM Tris / HCl, 250 mM NaCl, 1 mM DTT, 1 mM EDTA, pH 7.3) was pre-incubated with 0.6 mM (5.1-fold molar excess) of A-86 (150 mM in DMSO) and 4 mM TCEP for 1 h. 0.1 ul of the protein solution was then mixed 0.1 ul of reservoir solution (0.01 M Ca-Chloride, 0.1 M MES/NaOH, pH 6.50, 1.2 M Na-Acetate) and equilibrated at 4 C over 0.06 ml of reservoir solution. Crystals were obtained using microseeding. Well diffracting crystals appeared within 4 days and grew to full size over 8 days
Crystal Properties Matthews coefficient Solvent content 3.84 68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.599 α = 90 b = 171.599 β = 90 c = 97.79 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100.15 PIXEL DECTRIS PILATUS3 2M 2017-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 3.17 30 89.7 0.156 3.6 1.5 16344
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.17 3.34 83.7 0.702 1.1 1.4
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 3BLH 3.17 30 15466 857 89.49 0.17497 0.17055 0.1818 0.25677 0.2579 RANDOM 86.514
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] -0.36 -0.18 -0.36 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.89 r_dihedral_angle_3_deg 15.414 r_dihedral_angle_4_deg 15.327 r_long_range_B_refined 6.639 r_long_range_B_other 6.569 r_dihedral_angle_1_deg 6.267 r_mcangle_it 3.514 r_mcangle_other 3.514 r_scangle_other 3.252 r_mcbond_it 2.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.89 r_dihedral_angle_3_deg 15.414 r_dihedral_angle_4_deg 15.327 r_long_range_B_refined 6.639 r_long_range_B_other 6.569 r_dihedral_angle_1_deg 6.267 r_mcangle_it 3.514 r_mcangle_other 3.514 r_scangle_other 3.252 r_mcbond_it 2.046 r_mcbond_other 2.044 r_scbond_it 1.865 r_scbond_other 1.86 r_angle_refined_deg 1.187 r_angle_other_deg 0.873 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4590 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement SCALA data scaling REFMAC phasing