3F5U

Crystal structure of the death associated protein kinase in complex with AMPPNP 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 NaCl, 2.2 M ammonium sulfate , VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
1.935.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.669α = 90
b = 62.461β = 90
c = 88.599γ = 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
1230990.0689.16.81851236.2
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)
22.0787.70.5463.26.6

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 1JKS2301752117521941990.180.1770.245RANDOM30.29
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]
1.08-0.1-0.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.803
r_dihedral_angle_4_deg22.44
r_dihedral_angle_3_deg17.429
r_dihedral_angle_1_deg6.717
r_scangle_it4.287
r_scbond_it2.834
r_mcangle_it1.831
r_angle_refined_deg1.773
r_mcbond_it1.156
r_symmetry_hbond_refined0.345
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.803
r_dihedral_angle_4_deg22.44
r_dihedral_angle_3_deg17.429
r_dihedral_angle_1_deg6.717
r_scangle_it4.287
r_scbond_it2.834
r_mcangle_it1.831
r_angle_refined_deg1.773
r_mcbond_it1.156
r_symmetry_hbond_refined0.345
r_nbtor_refined0.311
r_symmetry_vdw_refined0.258
r_nbd_refined0.229
r_xyhbond_nbd_refined0.155
r_chiral_restr0.134
r_bond_refined_d0.018
r_gen_planes_refined0.007
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 Atoms2453
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms37

Software

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