3UBD

Structure of N-terminal domain of RSK2 kinase in complex with flavonoid glycoside SL0101


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3G51PDB ENTRY 3G51

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1hanging drop72930.1 M HEPES pH 7.0, 30% Jeffamine ED2003, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1743.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.446α = 90
b = 40.7β = 114.54
c = 83.354γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-06-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.000APS22-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
11.533099.50.06212.84.546748462015
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)
11.531.5695.10.4712.7

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 3G511.5324.44674844706225495.660.19490.19340.2226
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]
2.903-2.22420.29-3.193
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.532
f_angle_d0.973
f_chiral_restr0.064
f_bond_d0.006
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2328
Nucleic Acid Atoms
Solvent Atoms337
Heterogen Atoms37

Software

Software
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection
DENZOdata reduction