6QTY

Non-phosphorylated human CLK1 in complex with an indole inhibitor to 1.65 Ang


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.527324% PEG 3350, 200mM MgCl2, 100mM Bis-Tris (pH 6.5)
Crystal Properties
Matthews coefficientSolvent content
2.4750.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.764α = 90
b = 68.764β = 90
c = 285.004γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2013-09-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.93ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.655099.60.103166.549449
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.68

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 REPLACEMENTTHROUGHOUT2VAG1.6547.5544954241395.950.138870.135490.20316RANDOM19.39
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]
-0.07-0.07-0.070.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.214
r_sphericity_free30.513
r_dihedral_angle_4_deg15.745
r_sphericity_bonded13.936
r_dihedral_angle_3_deg12.708
r_scangle_other5.958
r_dihedral_angle_1_deg5.781
r_long_range_B_refined5.663
r_long_range_B_other5.545
r_scbond_it5.513
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.214
r_sphericity_free30.513
r_dihedral_angle_4_deg15.745
r_sphericity_bonded13.936
r_dihedral_angle_3_deg12.708
r_scangle_other5.958
r_dihedral_angle_1_deg5.781
r_long_range_B_refined5.663
r_long_range_B_other5.545
r_scbond_it5.513
r_scbond_other5.512
r_rigid_bond_restr5.416
r_mcangle_other3.672
r_mcangle_it3.67
r_mcbond_it3.041
r_mcbond_other3.038
r_angle_refined_deg1.859
r_angle_other_deg0.908
r_chiral_restr0.125
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.001
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2737
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing