6YTD

CLK1 V324A mutant bound with benzothiazole Tg003 (Cpd 2)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP727717% PEG 3350, 0,2M Na malonate
Crystal Properties
Matthews coefficientSolvent content
2.6954.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.917α = 90
b = 64.702β = 114.74
c = 89.344γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2018-03-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.91BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
1248.5697.10.0970.1060.0430.99610.2627570
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.05980.6180.6750.2680.8516.2

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 REPLACEMENTTHROUGHOUT1z57245.8126239132996.810.18180.17940.228RANDOM28.811
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]
0.83-0.11-1.590.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.354
r_dihedral_angle_4_deg19.782
r_dihedral_angle_3_deg14.236
r_dihedral_angle_1_deg7.161
r_angle_refined_deg1.584
r_angle_other_deg1.312
r_chiral_restr0.083
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.354
r_dihedral_angle_4_deg19.782
r_dihedral_angle_3_deg14.236
r_dihedral_angle_1_deg7.161
r_angle_refined_deg1.584
r_angle_other_deg1.312
r_chiral_restr0.083
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2770
Nucleic Acid Atoms
Solvent Atoms254
Heterogen Atoms17

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing