9MIU

Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound MW01-9-039SRM.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4YPD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8292Protein: 6.6 mg/ml, 0.25M Sodium chloride, 0.1M Tris-HCl (pH 8.0); Screen: 1.8M Ammomium sulfate, 0.2M Ammonium chloride; Soak: 24h, 1mM MW01-9-039SRM, 10% DMSO, 1.8M Ammonium sulfate, 0.2M Ammonium chloride; Cryo: 1.8M Ammonium sulfate, 25% sucrose.
Crystal Properties
Matthews coefficientSolvent content
1.9737.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.986α = 90
b = 62.627β = 90
c = 88.501γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2020-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (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
11.9301000.1220.1220.0490.99118.37.221300-325.3
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)
11.91.931000.5510.6612.36.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.929.5220177104699.930.159180.157350.19671RANDOM30.311
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]
1.74-0.12-1.62
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined8.84
r_long_range_B_other8.566
r_dihedral_angle_3_deg7.868
r_scangle_other6.534
r_scbond_it4.344
r_scbond_other4.131
r_mcangle_it3.585
r_mcangle_other3.585
r_dihedral_angle_1_deg3.386
r_mcbond_it2.454
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined8.84
r_long_range_B_other8.566
r_dihedral_angle_3_deg7.868
r_scangle_other6.534
r_scbond_it4.344
r_scbond_other4.131
r_mcangle_it3.585
r_mcangle_other3.585
r_dihedral_angle_1_deg3.386
r_mcbond_it2.454
r_mcbond_other2.45
r_dihedral_angle_2_deg2.031
r_angle_refined_deg1.588
r_angle_other_deg0.521
r_chiral_restr0.085
r_gen_planes_refined0.017
r_gen_planes_other0.014
r_bond_refined_d0.005
r_bond_other_d0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2238
Nucleic Acid Atoms
Solvent Atoms142
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing