4F6W

Crystal structure of human CDK8/CYCC in complex with compound 1 (N-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-4-[2-({[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]carbamoyl}amino)ethyl]piperazine-1-carboxamide)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3RGFPDB ENTRY 3RGF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.9293.1520% PEG3350, 0.2 M sodium formate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.7254.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.123α = 90
b = 71.71β = 90
c = 171.871γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-11-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.00002SLSX06SA

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
12.3985.941000.0828.13559335593
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)
12.392.581000.5948.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3RGF2.3985.943559334411118199.970.193190.193190.191760.2335RANDOM45.688
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]
0.06-1.221.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.509
r_dihedral_angle_4_deg14.735
r_dihedral_angle_3_deg12.978
r_scangle_it6.388
r_dihedral_angle_1_deg5.768
r_scbond_it4.352
r_mcangle_it2.899
r_mcbond_it1.66
r_angle_refined_deg1.273
r_angle_other_deg1.068
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.509
r_dihedral_angle_4_deg14.735
r_dihedral_angle_3_deg12.978
r_scangle_it6.388
r_dihedral_angle_1_deg5.768
r_scbond_it4.352
r_mcangle_it2.899
r_mcbond_it1.66
r_angle_refined_deg1.273
r_angle_other_deg1.068
r_mcbond_other0.431
r_chiral_restr0.076
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_gen_planes_other0.006
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4951
Nucleic Acid Atoms
Solvent Atoms150
Heterogen Atoms102

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling