2PO0

Crystal structure of the P. abyssi exosome RNase PH ring complexed with ADP in double conformation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PNZPDB ENTRY 2PNZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62910.1 M Bis-Tris, 45% MPD and 0.1 M LiCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Crystal Properties
Matthews coefficientSolvent content
2.8356.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.2α = 90
b = 94.2β = 90
c = 127.7γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2006-05-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE D03B-MX11.427LNLSD03B-MX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.344.2397.50.09316.59.729661289331141.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.32.4489.60.4513.78.44220

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2PNZ2.319.98112802626541143394.70.192810.192810.190190.24253RANDOM38.197
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]
-0.01-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.861
r_dihedral_angle_4_deg21.796
r_dihedral_angle_3_deg20.148
r_dihedral_angle_1_deg7.477
r_scangle_it3.208
r_scbond_it2.244
r_angle_refined_deg2.156
r_mcangle_it1.148
r_mcbond_it0.751
r_nbtor_refined0.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.861
r_dihedral_angle_4_deg21.796
r_dihedral_angle_3_deg20.148
r_dihedral_angle_1_deg7.477
r_scangle_it3.208
r_scbond_it2.244
r_angle_refined_deg2.156
r_mcangle_it1.148
r_mcbond_it0.751
r_nbtor_refined0.316
r_symmetry_vdw_refined0.25
r_nbd_refined0.241
r_symmetry_hbond_refined0.222
r_xyhbond_nbd_refined0.213
r_chiral_restr0.13
r_bond_refined_d0.021
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3900
Nucleic Acid Atoms
Solvent Atoms175
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling
MOLREPphasing