9T47 | pdb_00009t47

Structure of the SUN4 domain from Saccharomyces cerevisiae


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.528150 mg/ml ScSUN4, 10% PEG 400, 0.1 M NaHEPES pH 7.5, 1.5 M ammonium sulphate
Crystal Properties
Matthews coefficientSolvent content
2.5351.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.4α = 90
b = 99.16β = 90
c = 102.19γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-02-18MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-41.0332ESRFID14-4

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
11.0536.7297.70.04919.97.514363012.09
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)
11.051.1185.80.5352.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONSADFREE R-VALUE1.129.90.14127573797599.610.12430.12320.12320.14160.141718.45
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
f_dihedral_angle_d11.6799
f_angle_d1.044
f_chiral_restr0.0923
f_plane_restr0.0093
f_bond_d0.0081
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2085
Nucleic Acid Atoms
Solvent Atoms432
Heterogen Atoms19

Software

Software
Software NamePurpose
XDSdata reduction
PHENIXrefinement
SCALAdata scaling
SHELXDEphasing
Cootmodel building