3DGK

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5295100 mM Tris pH 7.5, 0.8 M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
1.9236.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.208α = 90
b = 62.441β = 90
c = 88.576γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDMirror2006-07-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.0000APS22-BM

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
11.75095.60.0744.82826828268-3
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)
11.71.7592.70.5262.33.42682

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 1jks1.725.522681726817143195.830.175340.172920.21999RANDOM20.727
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]
0.28-0.13-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.251
r_dihedral_angle_4_deg18.453
r_dihedral_angle_3_deg11.168
r_scangle_it4.615
r_dihedral_angle_1_deg4.48
r_scbond_it2.977
r_mcangle_it1.798
r_angle_refined_deg1.53
r_mcbond_it1.152
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.251
r_dihedral_angle_4_deg18.453
r_dihedral_angle_3_deg11.168
r_scangle_it4.615
r_dihedral_angle_1_deg4.48
r_scbond_it2.977
r_mcangle_it1.798
r_angle_refined_deg1.53
r_mcbond_it1.152
r_nbtor_refined0.31
r_nbd_refined0.231
r_symmetry_vdw_refined0.218
r_symmetry_hbond_refined0.203
r_xyhbond_nbd_refined0.175
r_chiral_restr0.11
r_bond_refined_d0.016
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2229
Nucleic Acid Atoms
Solvent Atoms221
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing