2CKE

Human death-associated DRP-1 kinase in complex with inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2A2APDB ENTRY 2A2A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.50.2 M LI SULFATE, 0.1 M TRIS PH 8.5, 25 % PEG 4000, 15 % GLYCEROL, 10 MM DTT.
Crystal Properties
Matthews coefficientSolvent content
2.3246.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.21α = 92.09
b = 60.48β = 103.39
c = 99.28γ = 94.16
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X13EMBL/DESY, HAMBURGX13

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
12.82097.50.0610.72.230010-3
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)
12.82.997.10.332.82.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB ENTRY 2A2A2.82028431149797.80.2060.2030.261RANDOM36.52
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]
1.670.10.72-1.031.74-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.914
r_dihedral_angle_4_deg15.684
r_dihedral_angle_3_deg14.269
r_dihedral_angle_1_deg5.103
r_angle_refined_deg0.882
r_scangle_it0.86
r_mcangle_it0.741
r_angle_other_deg0.738
r_scbond_it0.559
r_mcbond_it0.425
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.914
r_dihedral_angle_4_deg15.684
r_dihedral_angle_3_deg14.269
r_dihedral_angle_1_deg5.103
r_angle_refined_deg0.882
r_scangle_it0.86
r_mcangle_it0.741
r_angle_other_deg0.738
r_scbond_it0.559
r_mcbond_it0.425
r_symmetry_vdw_other0.2
r_nbd_refined0.189
r_nbtor_refined0.172
r_nbd_other0.168
r_symmetry_vdw_refined0.152
r_xyhbond_nbd_refined0.117
r_nbtor_other0.079
r_symmetry_hbond_refined0.062
r_chiral_restr0.051
r_bond_refined_d0.006
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9776
Nucleic Acid Atoms
Solvent Atoms60
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing