9DUE | pdb_00009due

Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound SRM-07-081a


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP292Protein: 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 SRM-7-081a, 10% DMSO, 1.8M Ammonium sulfate, 0.2M Ammonium chloride; Cryo: 1.8M Ammonium sulfate, 25% sucrose.
Crystal Properties
Matthews coefficientSolvent content
1.9336.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.01α = 90
b = 62.684β = 90
c = 88.462γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2019-11-14MSINGLE 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)Rrim I (All)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
11.65301000.0570.0570.0620.0230.99828.37.232407-322.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.681000.8810.8810.9610.3780.6832.16.3

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.6529.5430598157799.970.155210.153750.16690.183520.1963RANDOM26.461
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]
-0.10.66-0.56
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined7.834
r_dihedral_angle_3_deg7.616
r_long_range_B_other7.612
r_scangle_other6.092
r_scbond_it4.028
r_scbond_other3.851
r_dihedral_angle_1_deg3.496
r_mcangle_it2.954
r_mcangle_other2.954
r_mcbond_it2.005
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined7.834
r_dihedral_angle_3_deg7.616
r_long_range_B_other7.612
r_scangle_other6.092
r_scbond_it4.028
r_scbond_other3.851
r_dihedral_angle_1_deg3.496
r_mcangle_it2.954
r_mcangle_other2.954
r_mcbond_it2.005
r_mcbond_other2.005
r_dihedral_angle_2_deg1.946
r_angle_refined_deg1.536
r_angle_other_deg0.503
r_chiral_restr0.081
r_gen_planes_refined0.018
r_gen_planes_other0.015
r_bond_refined_d0.004
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 Atoms202
Heterogen Atoms49

Software

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