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CDK9/cyclin T1 in complex with KB-0742
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 277 0.2M K3 citrate, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 4 69.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.502 α = 90 b = 171.502 β = 90 c = 96.122 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 PIXEL DECTRIS EIGER X 16M 2021-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.99999 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.75 85.751 99.7 0.062 11.6 4.7 10792
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.75 4.19 0.683
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.751 85.751 10789 537 99.732 0.203 0.2002 0.2007 0.2455 0.2433 200.665
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] -2.508 -1.254 -2.508 8.135
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.833 r_lrange_other 19.832 r_mcangle_it 15.465 r_mcangle_other 15.462 r_scangle_it 13.963 r_scangle_other 13.962 r_dihedral_angle_3_deg 13.49 r_dihedral_angle_6_deg 11.492 r_mcbond_it 9.719 r_mcbond_other 9.719
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.833 r_lrange_other 19.832 r_mcangle_it 15.465 r_mcangle_other 15.462 r_scangle_it 13.963 r_scangle_other 13.962 r_dihedral_angle_3_deg 13.49 r_dihedral_angle_6_deg 11.492 r_mcbond_it 9.719 r_mcbond_other 9.719 r_scbond_it 8.465 r_scbond_other 8.463 r_dihedral_angle_1_deg 6.612 r_dihedral_angle_2_deg 2.549 r_angle_refined_deg 0.856 r_angle_other_deg 0.3 r_nbd_refined 0.234 r_nbd_other 0.231 r_symmetry_nbd_refined 0.222 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.131 r_symmetry_xyhbond_nbd_other 0.096 r_symmetry_xyhbond_nbd_refined 0.096 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.039 r_bond_other_d 0.004 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4537 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing