4F70

Crystal structure of human CDK8/CYCC in complex with compound 4 (1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-[2-(morpholin-4-yl)ethyl]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
2.7254.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.487α = 90
b = 71.847β = 90
c = 171.042γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-11-23MSINGLE 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
1385.5299.90.1146.281829218292
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)
133.2499.70.5111.58.3

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 3RGF385.52182921761063099.950.203810.203810.202560.23852RANDOM49.997
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]
-1.98-0.12.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.903
r_dihedral_angle_4_deg12.76
r_dihedral_angle_3_deg12.333
r_dihedral_angle_1_deg5.544
r_scangle_it3.011
r_scbond_it1.91
r_mcangle_it1.456
r_mcbond_it1.262
r_angle_refined_deg1.088
r_angle_other_deg0.892
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.903
r_dihedral_angle_4_deg12.76
r_dihedral_angle_3_deg12.333
r_dihedral_angle_1_deg5.544
r_scangle_it3.011
r_scbond_it1.91
r_mcangle_it1.456
r_mcbond_it1.262
r_angle_refined_deg1.088
r_angle_other_deg0.892
r_nbd_refined0.162
r_nbtor_refined0.16
r_symmetry_vdw_other0.145
r_mcbond_other0.144
r_symmetry_vdw_refined0.136
r_nbd_other0.125
r_xyhbond_nbd_refined0.1
r_symmetry_hbond_refined0.093
r_nbtor_other0.074
r_chiral_restr0.062
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4919
Nucleic Acid Atoms
Solvent Atoms32
Heterogen Atoms32

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling