4F7N

Crystal structure of human CDK8/CYCC in complex with compound 11 (1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-(5-hydroxypentyl)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
2.8957.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.157α = 90
b = 71.76β = 90
c = 180.362γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-04-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.00001SLSX06SA

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
12.6590.1999.70.0768.53.72786327863
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)
12.652.8699.60.5151.43.7

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 3RGF2.6590.19278632689990899.630.199860.199860.198930.22794RANDOM59.491
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]
1.43-1.780.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.138
r_dihedral_angle_4_deg15.202
r_dihedral_angle_3_deg12.227
r_dihedral_angle_1_deg5.29
r_scangle_it3.803
r_scbond_it2.607
r_mcangle_it1.741
r_mcbond_it1.418
r_angle_refined_deg1.178
r_angle_other_deg0.931
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.138
r_dihedral_angle_4_deg15.202
r_dihedral_angle_3_deg12.227
r_dihedral_angle_1_deg5.29
r_scangle_it3.803
r_scbond_it2.607
r_mcangle_it1.741
r_mcbond_it1.418
r_angle_refined_deg1.178
r_angle_other_deg0.931
r_mcbond_other0.212
r_nbd_refined0.171
r_nbtor_refined0.162
r_symmetry_vdw_other0.133
r_nbd_other0.132
r_symmetry_hbond_refined0.129
r_xyhbond_nbd_refined0.108
r_symmetry_vdw_refined0.083
r_nbtor_other0.075
r_chiral_restr0.068
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4993
Nucleic Acid Atoms
Solvent Atoms61
Heterogen Atoms34

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling