X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BLH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.3277.15CDK9/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 coefficientSolvent content
3.8468

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 171.599α = 90
b = 171.599β = 90
c = 97.79γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100.15PIXELDECTRIS PILATUS3 2M2017-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.966ESRFMASSIF-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
13.173089.70.1563.61.516344
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.173.3483.70.7021.11.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3BLH3.17301546685789.490.174970.170550.25677RANDOM86.514
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]
-0.36-0.18-0.361.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.89
r_dihedral_angle_3_deg15.414
r_dihedral_angle_4_deg15.327
r_long_range_B_refined6.639
r_long_range_B_other6.569
r_dihedral_angle_1_deg6.267
r_mcangle_it3.514
r_mcangle_other3.514
r_scangle_other3.252
r_mcbond_it2.046
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.89
r_dihedral_angle_3_deg15.414
r_dihedral_angle_4_deg15.327
r_long_range_B_refined6.639
r_long_range_B_other6.569
r_dihedral_angle_1_deg6.267
r_mcangle_it3.514
r_mcangle_other3.514
r_scangle_other3.252
r_mcbond_it2.046
r_mcbond_other2.044
r_scbond_it1.865
r_scbond_other1.86
r_angle_refined_deg1.187
r_angle_other_deg0.873
r_chiral_restr0.064
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms4590
Nucleic Acid Atoms
Solvent Atoms162
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
REFMACphasing