6HM5

Crystal structure of TOPBP1 BRCT0,1,2 in complex with a RAD9 phosphopeptide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP287.15100 mM bicine/Trizma base pH 8.5, 300 mM diethyleneglycol, 300 mM triethyleneglycol, 300 mM tetraethyleneglycol, 300 mM pentaethyleneglycol, 10% w/v PEG 20000 and 20% v/v PEG MME 550
Crystal Properties
Matthews coefficientSolvent content
2.2144.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.05α = 90
b = 34.07β = 103.57
c = 66.67γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.91407DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.3338.798.979.7231124239.53
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.332.413

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONFREE R-VALUE2.3300381222638.69918698141.3435325168211242112599.00484368120.2053369551880.2012706132670.24149121609651.5979895974
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.2843270689
f_angle_d0.516354821875
f_chiral_restr0.0429592405889
f_plane_restr0.00252518089053
f_bond_d0.00243241245682
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2056
Nucleic Acid Atoms
Solvent Atoms59
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing