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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
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 20% PEG 3350, 1% Tryptone, and 0.1 M HEPES at pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.48 64.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.963 α = 90 b = 73.963 β = 90 c = 176.251 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M Rh coated flat mirror 2009-12-05 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL DECTRIS PILATUS 6M Rh coated flat mirror 2009-12-05 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.84917 SSRL BL11-1 2 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97891, 0.91837, 0.97939 SSRL BL11-1
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1,2 2.7 50 99.9 0.033 0.043 5.8 13.5 8414 10.2 595.3
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) Redundancy Number Unique Reflections (All) 1,2 2.7 2.75 100 0.299 0.315 42.3 13.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.706 36.32 8310 7900 410 99.14 0.19394 0.19286 0.2062 0.21442 0.2269 RANDOM 63.971
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] 0.81 0.41 0.81 -1.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.384 r_dihedral_angle_4_deg 21.798 r_dihedral_angle_3_deg 16.337 r_scangle_it 6.472 r_dihedral_angle_1_deg 6.429 r_scbond_it 3.697 r_mcangle_it 3.536 r_mcbond_it 1.964 r_angle_refined_deg 1.496 r_angle_other_deg 0.868
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.384 r_dihedral_angle_4_deg 21.798 r_dihedral_angle_3_deg 16.337 r_scangle_it 6.472 r_dihedral_angle_1_deg 6.429 r_scbond_it 3.697 r_mcangle_it 3.536 r_mcbond_it 1.964 r_angle_refined_deg 1.496 r_angle_other_deg 0.868 r_mcbond_other 0.114 r_chiral_restr 0.082 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 1329 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 5
Software Software Software Name Purpose Blu-Ice data collection AutoSol phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling