2JA9

Structure of the N-terminal deletion of yeast exosome component Rrp40


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
120% (W/V) PEG 3350,200 MM NA2SO4
Crystal Properties
Matthews coefficientSolvent content
3.665.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 153.51α = 90
b = 153.51β = 90
c = 153.51γ = 90
Symmetry
Space GroupI 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SASLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.250990.12344515115
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.297.20.598.936

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.214.91151157961000.190.1890.206RANDOM42.22
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.609
r_dihedral_angle_4_deg14.937
r_dihedral_angle_3_deg13.191
r_dihedral_angle_1_deg5.732
r_scangle_it1.482
r_scbond_it1.005
r_angle_refined_deg0.997
r_mcangle_it0.714
r_angle_other_deg0.71
r_mcbond_it0.654
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.609
r_dihedral_angle_4_deg14.937
r_dihedral_angle_3_deg13.191
r_dihedral_angle_1_deg5.732
r_scangle_it1.482
r_scbond_it1.005
r_angle_refined_deg0.997
r_mcangle_it0.714
r_angle_other_deg0.71
r_mcbond_it0.654
r_symmetry_vdw_other0.228
r_symmetry_vdw_refined0.192
r_nbd_refined0.183
r_nbtor_refined0.174
r_nbd_other0.157
r_symmetry_hbond_refined0.132
r_xyhbond_nbd_refined0.131
r_nbtor_other0.076
r_mcbond_other0.066
r_chiral_restr0.06
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1338
Nucleic Acid Atoms
Solvent Atoms96
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
SHELXphasing