6Z53

Crystal structure of CLK3 in complex with macrocycle ODS2003128


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2EU9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277.1520% PEG 3350, 0.2 M Na/K phosphate, 10% ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
2.4850.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.995α = 90
b = 62.5β = 97.67
c = 76.027γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2012-05-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9200DiamondI04-1

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
11.6537.8796.40.0530.0650.03610.52.948435
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)
11.651.7497.40.5850.5850.7150.4042.52.9

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 REPLACEMENTTHROUGHOUT2eu91.6537.8745983244395.890.16850.1670.1945RANDOM16.945
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]
0.580.49-0.460.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.918
r_dihedral_angle_4_deg18.724
r_dihedral_angle_3_deg13.342
r_dihedral_angle_1_deg5.516
r_angle_refined_deg1.733
r_angle_other_deg0.992
r_chiral_restr0.117
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.918
r_dihedral_angle_4_deg18.724
r_dihedral_angle_3_deg13.342
r_dihedral_angle_1_deg5.516
r_angle_refined_deg1.733
r_angle_other_deg0.992
r_chiral_restr0.117
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2896
Nucleic Acid Atoms
Solvent Atoms391
Heterogen Atoms98

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing