2VGM

Structure of S. cerevisiae Dom34, a translation termination-like factor involved in RNA quality control pathways and interacting with Hbs1 (Unlabeled protein)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.77.5% POLYETHYLENE GLYCOL 4000, 50MM NAH2PO4 PH 6.7, 3% XYLITOL
Crystal Properties
Matthews coefficientSolvent content
3.260

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.5α = 90
b = 75.5β = 90
c = 163.981γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2007-03-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30AESRFBM30A

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
12.63598.70.111.32.916966-3
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)
12.62.7499.90.491.42.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONSADTHROUGHOUTNONE2.6352904514520.230.2260.2260.288RANDOM65
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
c_angle_deg1.079
c_bond_d0.007
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_scangle_it
c_angle_deg_na
c_angle_deg_prot
c_bond_d_na
RMS Deviations
KeyRefinement Restraint Deviation
c_angle_deg1.079
c_bond_d0.007
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_scangle_it
c_angle_deg_na
c_angle_deg_prot
c_bond_d_na
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_dihedral_angle_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2840
Nucleic Acid Atoms
Solvent Atoms26
Heterogen Atoms

Software

Software
Software NamePurpose
CNSrefinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing