3DFC

Crystal structure of a glycine-rich loop mutant of the death associated protein kinase catalytic domain with AMPPNP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JKSPDB entry 1jks

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2950.2M lithium nitrate, 2.2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
1.935.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.688α = 90
b = 62.444β = 90
c = 88.602γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBe-lenses2008-04-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.9786APS21-ID-G

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
11.9501000.087.22112921129-3
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)
11.91.971000.6053.27.32071

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1jks1.9301918419184102895.980.167930.164760.23048RANDOM24.481
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]
0.07-0.03-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.807
r_dihedral_angle_3_deg13.433
r_dihedral_angle_4_deg12.815
r_dihedral_angle_1_deg4.664
r_scangle_it4.3
r_scbond_it2.656
r_mcangle_it1.81
r_angle_refined_deg1.546
r_mcbond_it1.14
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.807
r_dihedral_angle_3_deg13.433
r_dihedral_angle_4_deg12.815
r_dihedral_angle_1_deg4.664
r_scangle_it4.3
r_scbond_it2.656
r_mcangle_it1.81
r_angle_refined_deg1.546
r_mcbond_it1.14
r_nbtor_refined0.312
r_symmetry_vdw_refined0.232
r_nbd_refined0.224
r_symmetry_hbond_refined0.19
r_xyhbond_nbd_refined0.164
r_chiral_restr0.125
r_bond_refined_d0.017
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2274
Nucleic Acid Atoms
Solvent Atoms188
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
BLU-MAXdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing