2PNZ

Crystal structure of the P. abyssi exosome RNase PH ring complexed with UDP and GMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BA0PDB ENTRY 2BA0

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
2.7855.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.81α = 90
b = 93.81β = 90
c = 126.26γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2006-04-01MSINGLE 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
12.1443.9899.30.17211.314.836300360601128
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)
2.142.26960.6393.311.85542

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 2BA02.1419.87113417433921178399.260.190880.190880.187520.25481RANDOM32.856
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]
-0.02-0.01-0.020.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.196
r_dihedral_angle_3_deg20.369
r_dihedral_angle_4_deg14.232
r_dihedral_angle_1_deg9.836
r_scangle_it4.074
r_scbond_it2.787
r_angle_refined_deg2.312
r_mcangle_it1.593
r_mcbond_it1.037
r_nbtor_refined0.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.196
r_dihedral_angle_3_deg20.369
r_dihedral_angle_4_deg14.232
r_dihedral_angle_1_deg9.836
r_scangle_it4.074
r_scbond_it2.787
r_angle_refined_deg2.312
r_mcangle_it1.593
r_mcbond_it1.037
r_nbtor_refined0.323
r_symmetry_vdw_refined0.252
r_nbd_refined0.243
r_xyhbond_nbd_refined0.195
r_symmetry_hbond_refined0.174
r_chiral_restr0.164
r_bond_refined_d0.023
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3913
Nucleic Acid Atoms
Solvent Atoms279
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling
MOLREPphasing