6T28

Crystal structure of human calmodulin-dependent protein kinase 1D (CAMK1D) bound to compound 19 (CS640)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JC6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.92930,1M NaCit, pH 5.9 2,05M AmmSO4 0,1M Na/K tartrate

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.64α = 90
b = 45.62β = 104.439
c = 108.949γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2017-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.91840BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.5533.886.20.99610.9434389
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.580.806

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2jc61.5531.7834359174185.8590.1590.15730.182919.177
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]
-0.359-0.702-0.260.866
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.29
r_dihedral_angle_4_deg18.153
r_dihedral_angle_3_deg12.889
r_dihedral_angle_1_deg6.46
r_lrange_it3.891
r_lrange_other3.84
r_scangle_it3.374
r_scangle_other3.373
r_mcangle_it3.136
r_mcangle_other3.135
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.29
r_dihedral_angle_4_deg18.153
r_dihedral_angle_3_deg12.889
r_dihedral_angle_1_deg6.46
r_lrange_it3.891
r_lrange_other3.84
r_scangle_it3.374
r_scangle_other3.373
r_mcangle_it3.136
r_mcangle_other3.135
r_scbond_it2.834
r_scbond_other2.833
r_mcbond_it2.337
r_mcbond_other2.336
r_rigid_bond_restr1.865
r_angle_refined_deg1.436
r_angle_other_deg1.41
r_nbd_refined0.21
r_nbd_other0.192
r_symmetry_nbd_other0.183
r_nbtor_refined0.173
r_symmetry_nbd_refined0.163
r_xyhbond_nbd_refined0.134
r_symmetry_xyhbond_nbd_refined0.127
r_symmetry_nbtor_other0.083
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2151
Nucleic Acid Atoms
Solvent Atoms125
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing