6I5H

Crystal structure of CLK1 in complex with furanopyrimidin VN412


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Z57 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP927723% PEG 6000, 0.1M bicine
Crystal Properties
Matthews coefficientSolvent content
2.5451.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.219α = 90
b = 64.049β = 111.99
c = 83.535γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97949DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
11.4968.2696.70.0740.0380.99710.45.262615
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.491.5294.50.8450.5491.55.3

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 REPLACEMENTTHROUGHOUT1z571.4949.4159474312596.440.179020.177620.20607RANDOM22.957
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]
0.030.27-1.661.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.448
r_dihedral_angle_4_deg24.581
r_dihedral_angle_3_deg11.514
r_dihedral_angle_1_deg6.23
r_long_range_B_refined5.675
r_long_range_B_other5.674
r_scangle_other2.88
r_scbond_it1.893
r_scbond_other1.892
r_mcangle_it1.847
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.448
r_dihedral_angle_4_deg24.581
r_dihedral_angle_3_deg11.514
r_dihedral_angle_1_deg6.23
r_long_range_B_refined5.675
r_long_range_B_other5.674
r_scangle_other2.88
r_scbond_it1.893
r_scbond_other1.892
r_mcangle_it1.847
r_mcangle_other1.846
r_angle_refined_deg1.734
r_mcbond_it1.185
r_mcbond_other1.185
r_angle_other_deg1.117
r_chiral_restr0.106
r_bond_refined_d0.014
r_gen_planes_refined0.011
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2592
Nucleic Acid Atoms
Solvent Atoms271
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing