2PO2

Crystal structure of the P. abyssi exosome RNase PH ring complexed with CDP


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
2.7555.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.498α = 90
b = 93.498β = 90
c = 125.714γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2006-05-20MSINGLE 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
12.443.6399.20.12411.15.525254250531140.3
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)
2.42.54960.6072.85.24012

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 2PNZ2.4119.8112388623727127399.320.186030.186030.182330.25852RANDOM36.625
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]
0.020.010.02-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.218
r_dihedral_angle_3_deg21.308
r_dihedral_angle_4_deg15.579
r_dihedral_angle_1_deg7.593
r_angle_refined_deg2.106
r_nbtor_refined0.324
r_nbd_refined0.242
r_xyhbond_nbd_refined0.192
r_chiral_restr0.127
r_bond_refined_d0.021
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.218
r_dihedral_angle_3_deg21.308
r_dihedral_angle_4_deg15.579
r_dihedral_angle_1_deg7.593
r_angle_refined_deg2.106
r_nbtor_refined0.324
r_nbd_refined0.242
r_xyhbond_nbd_refined0.192
r_chiral_restr0.127
r_bond_refined_d0.021
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3903
Nucleic Acid Atoms
Solvent Atoms216
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling
MOLREPphasing