3F5G

Crystal structure of death associated protein kinase in complex with ADP and Mg2+


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
12950.2 M ammonium chloride, 2.2 M ammonium sulfate , VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
1.9135.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.807α = 90
b = 62.545β = 90
c = 88.396γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBE LENSES2008-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-GAPS21-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
11.853098.10.06610.63.82239632
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)
1.851.9296.30.4694.153.8

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 1JKS1.85302120621206114798.10.1880.1850.244RANDOM25.72
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]
-0.040.51-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.681
r_dihedral_angle_4_deg17.414
r_dihedral_angle_3_deg16.166
r_dihedral_angle_1_deg6.971
r_scangle_it4.237
r_scbond_it2.727
r_mcangle_it1.682
r_angle_refined_deg1.572
r_mcbond_it1.034
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.681
r_dihedral_angle_4_deg17.414
r_dihedral_angle_3_deg16.166
r_dihedral_angle_1_deg6.971
r_scangle_it4.237
r_scbond_it2.727
r_mcangle_it1.682
r_angle_refined_deg1.572
r_mcbond_it1.034
r_nbtor_refined0.31
r_symmetry_vdw_refined0.229
r_nbd_refined0.22
r_xyhbond_nbd_refined0.159
r_symmetry_hbond_refined0.155
r_chiral_restr0.109
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2434
Nucleic Acid Atoms
Solvent Atoms133
Heterogen Atoms28

Software

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