3BHY

Crystal structure of human death associated protein kinase 3 (DAPK3) in complex with a beta-carboline ligand


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62770.1M SPG (sucrose-phosphate-glutamate buffer) pH 6.0, 30% PEG 1000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
1.9135.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.549α = 90
b = 90.68β = 100.45
c = 41.464γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-11-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.97926SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.245099.50.0790.07914.73.76864268318
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.241.281000.7070.7072.043.66829

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1YRP1.2445.366831768317345399.530.1460.1460.1430.187RANDOM15.982
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]
0.34-0.06-0.420.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.863
r_sphericity_free19.814
r_dihedral_angle_4_deg19.334
r_dihedral_angle_3_deg12.942
r_scangle_it10.898
r_scbond_it8.964
r_sphericity_bonded8.856
r_mcangle_it6.382
r_dihedral_angle_1_deg5.657
r_mcbond_it5.528
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.863
r_sphericity_free19.814
r_dihedral_angle_4_deg19.334
r_dihedral_angle_3_deg12.942
r_scangle_it10.898
r_scbond_it8.964
r_sphericity_bonded8.856
r_mcangle_it6.382
r_dihedral_angle_1_deg5.657
r_mcbond_it5.528
r_rigid_bond_restr4.887
r_mcbond_other3.402
r_angle_other_deg1.996
r_angle_refined_deg1.703
r_nbd_refined0.249
r_symmetry_vdw_other0.219
r_nbd_other0.192
r_nbtor_refined0.184
r_symmetry_hbond_refined0.173
r_xyhbond_nbd_refined0.157
r_symmetry_vdw_refined0.135
r_chiral_restr0.128
r_nbtor_other0.095
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2109
Nucleic Acid Atoms
Solvent Atoms301
Heterogen Atoms26

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction