6K3L

Crystal structure of CX-4945 bound Cka1 from C. neoformans


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LP4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52900.2 M lithium sulfate, 0.1 M Tris pH 8.5, 30 %(w/v) PEG 4000, 30%(w/v) dextran sulfate sodium salt, 5mM CX-4945
Crystal Properties
Matthews coefficientSolvent content
2.6152.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.762α = 90
b = 95.395β = 90
c = 94.518γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-05-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 11C0.97PAL/PLS11C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.0965.79970.025060.99915.7223770
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)
12.0942.1690.26720.884

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 REPLACEMENTTHROUGHOUT1LP42.0947.7421739199596.810.189360.186730.2186RANDOM36.927
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]
-0.020.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.553
r_dihedral_angle_4_deg22.358
r_dihedral_angle_3_deg13.988
r_long_range_B_refined8.172
r_long_range_B_other8.171
r_scangle_other6.097
r_dihedral_angle_1_deg5.905
r_scbond_it4.001
r_scbond_other4.001
r_mcangle_it3.871
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.553
r_dihedral_angle_4_deg22.358
r_dihedral_angle_3_deg13.988
r_long_range_B_refined8.172
r_long_range_B_other8.171
r_scangle_other6.097
r_dihedral_angle_1_deg5.905
r_scbond_it4.001
r_scbond_other4.001
r_mcangle_it3.871
r_mcangle_other3.87
r_mcbond_it2.763
r_mcbond_other2.763
r_angle_refined_deg1.609
r_angle_other_deg1.495
r_chiral_restr0.088
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.002
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 Atoms2739
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing