3UXU

The structure of the catalytic domain of the Sulfolobus Spindle-shaped viral integrase reveals an evolutionarily conserved catalytic core and supports a mechanism of DNA cleavage in trans


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729520% PEG 3350, 1% Tryptone, and 0.1 M HEPES at pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.4864.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.963α = 90
b = 73.963β = 90
c = 176.251γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MRh coated flat mirror2009-12-05MSINGLE WAVELENGTH
21x-ray100PIXELDECTRIS PILATUS 6MRh coated flat mirror2009-12-05MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.84917SSRLBL11-1
2SYNCHROTRONSSRL BEAMLINE BL11-10.97891, 0.91837, 0.97939SSRLBL11-1

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
1,22.75099.90.0330.0435.813.5841410.2595.3
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)
1,22.72.751000.2990.31542.313.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)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 DIFFRACTIONMADTHROUGHOUT2.70636.328310790041099.140.193940.192860.21442RANDOM63.971
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]
0.810.410.81-1.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.384
r_dihedral_angle_4_deg21.798
r_dihedral_angle_3_deg16.337
r_scangle_it6.472
r_dihedral_angle_1_deg6.429
r_scbond_it3.697
r_mcangle_it3.536
r_mcbond_it1.964
r_angle_refined_deg1.496
r_angle_other_deg0.868
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.384
r_dihedral_angle_4_deg21.798
r_dihedral_angle_3_deg16.337
r_scangle_it6.472
r_dihedral_angle_1_deg6.429
r_scbond_it3.697
r_mcangle_it3.536
r_mcbond_it1.964
r_angle_refined_deg1.496
r_angle_other_deg0.868
r_mcbond_other0.114
r_chiral_restr0.082
r_bond_refined_d0.018
r_gen_planes_refined0.006
r_bond_other_d0.005
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1329
Nucleic Acid Atoms
Solvent Atoms17
Heterogen Atoms5

Software

Software
Software NamePurpose
Blu-Icedata collection
AutoSolphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling