6SCE

Structure of a Type III CRISPR defence DNA nuclease activated by cyclic oligoadenylate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529320% PEG 3350, 0.2 M sodium citrate, 0.1 M bis-Tris propane, pH 6.5
Crystal Properties
Matthews coefficientSolvent content
3.1561.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.37α = 90
b = 84.52β = 90
c = 123.1γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9159DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.8259.71000.070.9991813.378941
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.831.861001.430.755213.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.8359.774943392199.950.178130.17650.20944RANDOM41.802
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]
-1.1-1.142.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.827
r_dihedral_angle_4_deg15.044
r_dihedral_angle_3_deg12.314
r_long_range_B_refined6.711
r_long_range_B_other6.711
r_dihedral_angle_1_deg5.737
r_scangle_other4.73
r_mcangle_it3.461
r_mcangle_other3.46
r_scbond_it3.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.827
r_dihedral_angle_4_deg15.044
r_dihedral_angle_3_deg12.314
r_long_range_B_refined6.711
r_long_range_B_other6.711
r_dihedral_angle_1_deg5.737
r_scangle_other4.73
r_mcangle_it3.461
r_mcangle_other3.46
r_scbond_it3.03
r_scbond_other3.03
r_mcbond_it2.458
r_mcbond_other2.457
r_angle_refined_deg1.422
r_angle_other_deg0.786
r_chiral_restr0.088
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4832
Nucleic Acid Atoms
Solvent Atoms412
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
AutoSolphasing