3DSC

Crystal structure of P. furiosus Mre11 DNA synaptic complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529320% PEG 1000, 0.1 M Tris-HCl, 0.2 M MgCl2, 0.2 M 1,6 hexanediol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1342.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.477α = 90
b = 106.071β = 90
c = 76.667γ = 90
Symmetry
Space GroupC 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.2ALS5.0.2

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
12.72094.50.08517.64.81076911

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1II72.719.9410769970854595.550.230340.230340.227560.27804RANDOM42.368
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]
-1.714.77-3.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.481
r_dihedral_angle_4_deg16.295
r_dihedral_angle_3_deg16.059
r_dihedral_angle_1_deg4.865
r_angle_refined_deg0.983
r_mcangle_it0.354
r_nbtor_refined0.31
r_symmetry_hbond_refined0.238
r_mcbond_it0.199
r_xyhbond_nbd_refined0.152
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.481
r_dihedral_angle_4_deg16.295
r_dihedral_angle_3_deg16.059
r_dihedral_angle_1_deg4.865
r_angle_refined_deg0.983
r_mcangle_it0.354
r_nbtor_refined0.31
r_symmetry_hbond_refined0.238
r_mcbond_it0.199
r_xyhbond_nbd_refined0.152
r_nbd_refined0.146
r_symmetry_vdw_refined0.129
r_scangle_it0.099
r_chiral_restr0.072
r_scbond_it0.06
r_bond_refined_d0.005
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2754
Nucleic Acid Atoms348
Solvent Atoms63
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing