4F6S

Crystal structure of human CDK8/CYCC in complex with compound 7 (1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]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
2.754.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.036α = 90
b = 71.395β = 90
c = 171.719γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-02-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.00000SLSX06SA

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
12.685.8699.90.09317.838.12758927589
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)
12.62.8199.70.63517.838.4

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3RGF2.685.86275892665293699.850.204690.202760.26028RANDOM54.424
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]
-1.1-2.013.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.271
r_dihedral_angle_4_deg15.41
r_dihedral_angle_3_deg12.884
r_scangle_it5.388
r_dihedral_angle_1_deg5.185
r_scbond_it3.585
r_mcangle_it2.459
r_mcbond_it1.378
r_angle_refined_deg1.018
r_angle_other_deg0.809
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.271
r_dihedral_angle_4_deg15.41
r_dihedral_angle_3_deg12.884
r_scangle_it5.388
r_dihedral_angle_1_deg5.185
r_scbond_it3.585
r_mcangle_it2.459
r_mcbond_it1.378
r_angle_refined_deg1.018
r_angle_other_deg0.809
r_mcbond_other0.286
r_chiral_restr0.06
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_gen_planes_other0.002
r_bond_other_d0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4925
Nucleic Acid Atoms
Solvent Atoms90
Heterogen Atoms57

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling