7PQ2

Crystal Structure of the Ring Nuclease 0811 from Sulfolobus islandicus (Sis0811) in its apo form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QYF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29330% PEG3000, 0.1M CHES pH 9.5
Crystal Properties
Matthews coefficientSolvent content
2.4950.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.372α = 90
b = 106.436β = 102.919
c = 78.443γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-11-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX0.98MAX IVBioMAX

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
12.3861.7399.90.9914.1724724
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)
12.382.430.756

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-VALUE3QYF2.3861.6123654117695.0840.1660.16340.222642.532
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]
0.0320.004-0.033-0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.116
r_dihedral_angle_4_deg21.626
r_dihedral_angle_3_deg18.298
r_lrange_it8.973
r_dihedral_angle_1_deg6.239
r_scangle_it5.916
r_mcangle_it4.043
r_scbond_it3.76
r_mcbond_it2.544
r_angle_refined_deg1.776
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.116
r_dihedral_angle_4_deg21.626
r_dihedral_angle_3_deg18.298
r_lrange_it8.973
r_dihedral_angle_1_deg6.239
r_scangle_it5.916
r_mcangle_it4.043
r_scbond_it3.76
r_mcbond_it2.544
r_angle_refined_deg1.776
r_nbtor_refined0.32
r_nbd_refined0.224
r_symmetry_nbd_refined0.193
r_xyhbond_nbd_refined0.165
r_symmetry_xyhbond_nbd_refined0.151
r_ncsr_local_group_10.14
r_chiral_restr0.124
r_bond_refined_d0.01
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4442
Nucleic Acid Atoms
Solvent Atoms254
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing