2A2A

High-resolution crystallographic analysis of the autoinhibited conformation of a human death-associated protein kinase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2A27 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5295PEG4000, glycerol, DTT, Tris, lithium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.243

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.3α = 92.16
b = 60.65β = 103.45
c = 98.71γ = 94.25
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2004-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7A0.9206EMBL/DESY, HAMBURGBW7A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.474094.80.04911.12.5200389200389-3-327
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.471.5293.40.4241.91.918844

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUT2A271.4720-3200335200335200394.820.150160.150160.149590.20688RANDOM23.625
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]
0.57-0.241.010.36-0.2-0.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.947
r_dihedral_angle_4_deg17.967
r_sphericity_free14.73
r_dihedral_angle_3_deg13.953
r_scangle_it9.187
r_scbond_it6.908
r_dihedral_angle_1_deg5.934
r_sphericity_bonded5.875
r_mcangle_it5.22
r_mcbond_it4.102
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.947
r_dihedral_angle_4_deg17.967
r_sphericity_free14.73
r_dihedral_angle_3_deg13.953
r_scangle_it9.187
r_scbond_it6.908
r_dihedral_angle_1_deg5.934
r_sphericity_bonded5.875
r_mcangle_it5.22
r_mcbond_it4.102
r_rigid_bond_restr3.578
r_mcbond_other2.061
r_angle_refined_deg1.599
r_angle_other_deg0.873
r_nbd_refined0.233
r_metal_ion_refined0.215
r_symmetry_vdw_other0.203
r_nbd_other0.188
r_symmetry_hbond_refined0.185
r_nbtor_refined0.178
r_xyhbond_nbd_refined0.176
r_chiral_restr0.107
r_symmetry_vdw_refined0.103
r_nbtor_other0.085
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9884
Nucleic Acid Atoms
Solvent Atoms1371
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing