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Crystal Structure of Human CDK9/cyclinT1 in complex with MC180295
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BLQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 277 0.1M Na/K phosphate pH6.2, 200mM NaCl, 4mM TCEP and 1~6% PEG1000
Crystal Properties Matthews coefficient Solvent content 4.13 70.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.34 α = 90 b = 173.34 β = 90 c = 97.368 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 9M 2018-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.97935 NSLS-II 17-ID-1
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 3.1 86.67 99.6 0.061 0.999 14.9 4.4 19797
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.18 96.6 0.885 0.566 1.2 4.5
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 3blq 3.1 86.67 18780 1014 99.6 0.175 0.172 0.1718 0.221 0.2167 RANDOM 107.3
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] -0.93 -0.47 -0.93 3.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.301 r_dihedral_angle_3_deg 18.686 r_dihedral_angle_4_deg 17.938 r_dihedral_angle_1_deg 6.94 r_angle_refined_deg 2.052 r_angle_other_deg 1.087 r_chiral_restr 0.09 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.301 r_dihedral_angle_3_deg 18.686 r_dihedral_angle_4_deg 17.938 r_dihedral_angle_1_deg 6.94 r_angle_refined_deg 2.052 r_angle_other_deg 1.087 r_chiral_restr 0.09 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4555 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing