6T29

Crystal structure of human calmodulin-dependent protein kinase 1D (CAMK1D) bound to compound 18 (CS587)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.92930,1M NaCit, pH 5.9 2,05M AmmSO4 0,1M Na/K tartrate

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.82α = 90
b = 45.64β = 104.183
c = 108.754γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-09-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.95372PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.4855.4598.70.0260.99914.86.344955
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.481.5198.30.1550.8834.26.6

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-VALUE2jc61.48455.44844954229198.4650.1370.13550.174717.818
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]
0.727-0.17-0.188-0.402
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.006
r_dihedral_angle_4_deg21.923
r_dihedral_angle_3_deg11.751
r_dihedral_angle_1_deg6.255
r_lrange_it3.535
r_lrange_other3.535
r_scangle_it2.815
r_scangle_other2.815
r_mcangle_it2.324
r_mcangle_other2.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.006
r_dihedral_angle_4_deg21.923
r_dihedral_angle_3_deg11.751
r_dihedral_angle_1_deg6.255
r_lrange_it3.535
r_lrange_other3.535
r_scangle_it2.815
r_scangle_other2.815
r_mcangle_it2.324
r_mcangle_other2.323
r_scbond_it2.231
r_scbond_other2.23
r_mcbond_it1.714
r_mcbond_other1.713
r_angle_other_deg1.416
r_angle_refined_deg1.409
r_rigid_bond_restr1.4
r_nbd_refined0.215
r_symmetry_nbd_refined0.187
r_symmetry_nbd_other0.175
r_nbtor_refined0.174
r_nbd_other0.163
r_symmetry_xyhbond_nbd_refined0.136
r_xyhbond_nbd_refined0.127
r_symmetry_nbtor_other0.084
r_chiral_restr0.069
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2175
Nucleic Acid Atoms
Solvent Atoms197
Heterogen Atoms73

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing