4F6U

Crystal structure of human CDK8/CYCC in complex with compound 5 (1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-[3-(morpholin-4-yl)propyl]urea)


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
2.6954.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.397α = 90
b = 71.024β = 90
c = 171.217γ = 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 X06SA0.99987SLSX06SA

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
12.185.6199.90.0658.15165251652
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)
12.12.271000.5498

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 3RGF2.185.615162649911171599.950.17720.17720.176490.19756RANDOM45.108
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]
-0.860.360.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.185
r_dihedral_angle_4_deg13.861
r_dihedral_angle_3_deg11.838
r_dihedral_angle_1_deg5.509
r_scangle_it5.509
r_scbond_it3.774
r_mcangle_it2.687
r_mcbond_it1.569
r_angle_refined_deg1.21
r_angle_other_deg1.019
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.185
r_dihedral_angle_4_deg13.861
r_dihedral_angle_3_deg11.838
r_dihedral_angle_1_deg5.509
r_scangle_it5.509
r_scbond_it3.774
r_mcangle_it2.687
r_mcbond_it1.569
r_angle_refined_deg1.21
r_angle_other_deg1.019
r_mcbond_other0.453
r_chiral_restr0.073
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_gen_planes_other0.005
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4986
Nucleic Acid Atoms
Solvent Atoms309
Heterogen Atoms92

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling