3EH9

Crystal structure of death associated protein kinase complexed with ADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JKSPDB Entry 1JKS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP295.2 M ammonium iodide 2.2 M ammonium sulfate , VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
1.9235.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.862α = 90
b = 62.675β = 90
c = 88.23γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBe lenses2008-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97857APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.7300.06612.73.82938329383-330.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.71.760.5014.083.72895

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB Entry 1JKS1.7302783527835148999.890.179550.177530.21706RANDOM24.628
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]
-0.220.54-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.525
r_dihedral_angle_4_deg17.203
r_dihedral_angle_3_deg14.455
r_dihedral_angle_1_deg6.098
r_scangle_it3.898
r_scbond_it2.387
r_mcangle_it1.562
r_angle_refined_deg1.47
r_mcbond_it0.94
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.525
r_dihedral_angle_4_deg17.203
r_dihedral_angle_3_deg14.455
r_dihedral_angle_1_deg6.098
r_scangle_it3.898
r_scbond_it2.387
r_mcangle_it1.562
r_angle_refined_deg1.47
r_mcbond_it0.94
r_nbtor_refined0.311
r_nbd_refined0.219
r_symmetry_vdw_refined0.207
r_symmetry_hbond_refined0.173
r_xyhbond_nbd_refined0.151
r_chiral_restr0.102
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2353
Nucleic Acid Atoms
Solvent Atoms208
Heterogen Atoms46

Software

Software
Software NamePurpose
BLU-MAXdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling