4PF4

1.1A X-RAY STRUCTURE OF THE APO CATALYTIC DOMAIN OF DEATH-ASSOCIATED PROTEIN KINASE 1, aa 1-277


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2W4J 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72920.1 M HEPES, Ph=7, 2M Ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
1.9938.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.516α = 90
b = 62.005β = 90
c = 88.375γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-04-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.973ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.12950.75899.40.0760.0820.03210.76.39600996009
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.131.1996.50.7090.7090.3411.1513431

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 REPLACEMENTTHROUGHOUT2W4J1.1350.75895914480599.360.11830.11670.1495RANDOM16.198
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]
-1.090.610.49
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free36.855
r_dihedral_angle_2_deg36.204
r_dihedral_angle_4_deg21.611
r_sphericity_bonded17.943
r_dihedral_angle_3_deg12.907
r_rigid_bond_restr6.955
r_dihedral_angle_1_deg6.164
r_angle_refined_deg2.184
r_angle_other_deg2.168
r_chiral_restr0.163
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free36.855
r_dihedral_angle_2_deg36.204
r_dihedral_angle_4_deg21.611
r_sphericity_bonded17.943
r_dihedral_angle_3_deg12.907
r_rigid_bond_restr6.955
r_dihedral_angle_1_deg6.164
r_angle_refined_deg2.184
r_angle_other_deg2.168
r_chiral_restr0.163
r_bond_refined_d0.024
r_gen_planes_refined0.012
r_gen_planes_other0.005
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2232
Nucleic Acid Atoms
Solvent Atoms489
Heterogen Atoms107

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
REFMACrefinement
XDSdata reduction
XSCALEdata reduction