6Z50

Crystal structure of CLK1 in complex with macrocycle ODS2003208


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6G33 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277.1523% PEG3350, 0.1M sodium malonate
Crystal Properties
Matthews coefficientSolvent content
2.8857.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.173α = 90
b = 69.173β = 90
c = 330.581γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2014-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97626DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.630.6599.90.0750.0770.01821.216.963327
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6999.20.5970.5970.6320.2033.39.2

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 REPLACEMENTTHROUGHOUT6g331.630.6560050312699.80.15220.15080.1795RANDOM22.633
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]
0.380.190.38-1.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.489
r_dihedral_angle_4_deg21.046
r_dihedral_angle_3_deg11.557
r_dihedral_angle_1_deg6.074
r_angle_refined_deg1.656
r_angle_other_deg0.839
r_chiral_restr0.113
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2735
Nucleic Acid Atoms
Solvent Atoms472
Heterogen Atoms120

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing