4Q10

The catalytic core of Rad2 in complex with DNA substrate (complex IV)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4Q0Rpdb entry 4Q0R

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52918% (w/v) PEG 8000, 18% (v/v) ethylene glycol, 0.2 M D-glucose, 0.2 M D-mannose, 0.2 M D-galactose, 0.2 M L-fructose, 0.2 M D-xylose, 0.2 M N-acetyl-D-glucosamine, and 0.1 M MOPS/HEPES-Na, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.7355

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.68α = 90
b = 97.958β = 96.41
c = 112.038γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2013-05-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.89440BESSY14.2

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
12.7111.395.520.07119.729227279181.91.9
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)
12.72.7599.90.6031.93.3

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 REPLACEMENTpdb entry 4Q0R2.743.1331.342922727918141495.520.23440.23160.2841random
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_d22.655
f_angle_d1.006
f_chiral_restr0.065
f_bond_d0.007
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4670
Nucleic Acid Atoms663
Solvent Atoms126
Heterogen Atoms4

Software

Software
Software NamePurpose
MAR345data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling