4BCI

Structure of CDK9 in complex with cyclin T and a 2-amino-4-heteroaryl- pyrimidine inhibitor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.2277CRYSTALS WERE GROWN AT 4C USING 10-16% PEG 1000, 100MM NAK-PHOSPHATE PH 6.2, 500MM NACL, 4MM TCEP AS THE PRECIPITANT SOLUTION. THEY WERE SUBSEQUENTLY SOAKED IN THE PRESENCE OF COMPOUND.
Crystal Properties
Matthews coefficientSolvent content
2.347

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 174.11α = 90
b = 174.11β = 90
c = 99.261γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.9760.0499.30.068.613.6320202
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.13.2799.50.591.293.68

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONOTHERTHROUGHOUT3.137.42820201102499.2920.180.17770.2213110.632
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]
-4.036-4.036-4.03613.093
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.551
r_dihedral_angle_4_deg16.85
r_dihedral_angle_3_deg15.486
r_mcangle_it13.678
r_scangle_it12.045
r_scbond_it7.943
r_mcbond_it6.644
r_dihedral_angle_1_deg4.964
r_mcbond_other1.688
r_angle_refined_deg1.125
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.551
r_dihedral_angle_4_deg16.85
r_dihedral_angle_3_deg15.486
r_mcangle_it13.678
r_scangle_it12.045
r_scbond_it7.943
r_mcbond_it6.644
r_dihedral_angle_1_deg4.964
r_mcbond_other1.688
r_angle_refined_deg1.125
r_angle_other_deg0.625
r_nbd_refined0.355
r_xyhbond_nbd_refined0.222
r_nbtor_refined0.207
r_nbd_other0.193
r_chiral_restr0.073
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbtor_other
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_mcangle_other
r_scbond_other
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 AtomsNumber
Protein Atoms4562
Nucleic Acid Atoms
Solvent Atoms8
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXphasing