X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1O9U 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529310% Isopropanol 20% PEG 4000 0.1 M NaHepes 7.5 4 mM indirubin E804 20% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2946.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.101α = 90
b = 138.366β = 90
c = 43.261γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2008-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.96749APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.655099.40.1890.11713.0836.7246912454347.77
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.652.7495.70.8010.5911.775.12313

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1o9u2.65352425324140123499.530.240.240.2380.295RANDOM21.267
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]
-1.512.34-0.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.47
r_dihedral_angle_4_deg20.449
r_dihedral_angle_3_deg18.136
r_dihedral_angle_1_deg5.821
r_scangle_it1.861
r_angle_refined_deg1.396
r_scbond_it1.148
r_mcangle_it0.743
r_mcbond_it0.422
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.47
r_dihedral_angle_4_deg20.449
r_dihedral_angle_3_deg18.136
r_dihedral_angle_1_deg5.821
r_scangle_it1.861
r_angle_refined_deg1.396
r_scbond_it1.148
r_mcangle_it0.743
r_mcbond_it0.422
r_nbtor_refined0.314
r_symmetry_hbond_refined0.262
r_nbd_refined0.212
r_symmetry_vdw_refined0.194
r_xyhbond_nbd_refined0.152
r_chiral_restr0.085
r_bond_refined_d0.011
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4965
Nucleic Acid Atoms
Solvent Atoms150
Heterogen Atoms78

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction