5ICP

CDK8-CYCC IN COMPLEX WITH [(S)-2-(4-Chloro-phenyl)-pyrrolidin-1-yl]-(5-methyl-imidazo[5,1-b][1,3,4]thiadiazol-2-yl)-methanone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4F6S 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.929320% PEG3350, 0.2 M sodium formate, pH 6.9
Crystal Properties
Matthews coefficientSolvent content
2.9558.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.39α = 90
b = 70.391β = 90
c = 168.739γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2013-12-01MSINGLE 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
12.1884.391000.08916.028.244584
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)
12.182.431000.5548.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4f6s2.1884.3943036154799.980.184590.183510.21571RANDOM52.441
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]
-1.44-0.361.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.528
r_dihedral_angle_4_deg14.573
r_dihedral_angle_3_deg11.406
r_dihedral_angle_1_deg5.537
r_angle_refined_deg1.124
r_angle_other_deg0.985
r_chiral_restr0.065
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.528
r_dihedral_angle_4_deg14.573
r_dihedral_angle_3_deg11.406
r_dihedral_angle_1_deg5.537
r_angle_refined_deg1.124
r_angle_other_deg0.985
r_chiral_restr0.065
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.001
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5057
Nucleic Acid Atoms
Solvent Atoms222
Heterogen Atoms62

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
BUSTERrefinement