7PQ3

Crystal Structure of the Ring Nuclease 0811 from Sulfolobus islandicus (Sis0811) in complex with its post-catalytic reaction product


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7PQ2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29320% PEG 3350, 0.1M Bis-Tris propane pH 7.5, 0.2M KSCN
Crystal Properties
Matthews coefficientSolvent content
2.346.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.731α = 90
b = 56.731β = 90
c = 361.469γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.8561.5293.50.999.37.814426
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.852.920.37

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7PQ22.8548.051403174099.1870.2540.25150.2906117.141
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]
-0.595-0.5951.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.572
r_dihedral_angle_3_deg21.725
r_dihedral_angle_4_deg18.63
r_lrange_it11.251
r_lrange_other11.25
r_dihedral_angle_1_deg6.863
r_scangle_it5.195
r_scangle_other5.194
r_mcangle_it4.716
r_mcangle_other4.716
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.572
r_dihedral_angle_3_deg21.725
r_dihedral_angle_4_deg18.63
r_lrange_it11.251
r_lrange_other11.25
r_dihedral_angle_1_deg6.863
r_scangle_it5.195
r_scangle_other5.194
r_mcangle_it4.716
r_mcangle_other4.716
r_scbond_it3.098
r_scbond_other3.098
r_mcbond_it2.763
r_mcbond_other2.763
r_angle_refined_deg1.638
r_angle_other_deg1.284
r_nbd_other0.233
r_symmetry_nbd_refined0.225
r_symmetry_nbd_other0.214
r_nbd_refined0.205
r_nbtor_refined0.174
r_ncsr_local_group_10.159
r_xyhbond_nbd_refined0.157
r_symmetry_nbtor_other0.083
r_chiral_restr0.081
r_symmetry_xyhbond_nbd_refined0.073
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4358
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing