6Z2V

CLK3 A319V mutant bound with beta-carboline KH-CARB13 (Cpd 3)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.527824% PEG 3350, 0,2M KSCN, 10% Ethylene Glycol, 0.1M bis-tris propane
Crystal Properties
Matthews coefficientSolvent content
2.2445.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.376α = 90
b = 45.393β = 111.16
c = 106.334γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2017-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.9184BESSY14.2

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
12.639.371000.2460.2660.1010.9856.46.911812
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)
12.62.721001.3191.4220.5270.5977.2

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 REPLACEMENTTHROUGHOUT2eu92.639.371125155999.930.20510.20190.2645RANDOM35.266
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]
-0.53-0.911.060.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.518
r_dihedral_angle_4_deg24.278
r_dihedral_angle_3_deg18.517
r_dihedral_angle_1_deg8.779
r_angle_refined_deg1.788
r_angle_other_deg1.33
r_chiral_restr0.082
r_bond_refined_d0.017
r_gen_planes_refined0.013
r_gen_planes_other0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.518
r_dihedral_angle_4_deg24.278
r_dihedral_angle_3_deg18.517
r_dihedral_angle_1_deg8.779
r_angle_refined_deg1.788
r_angle_other_deg1.33
r_chiral_restr0.082
r_bond_refined_d0.017
r_gen_planes_refined0.013
r_gen_planes_other0.007
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2743
Nucleic Acid Atoms
Solvent Atoms61
Heterogen Atoms29

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing