3CRR

Structure of tRNA Dimethylallyltransferase: RNA Modification through a Channel


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5278PEG 6000, pH 8.5, vapor diffusion, hanging drop, temperature 278K
Crystal Properties
Matthews coefficientSolvent content
2.3447.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.23α = 90
b = 76.23β = 90
c = 57.809γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD2006-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM0.98APS22-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.9502628125456

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTION1.950122653176886.20.2090.23538.884
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]
6.576.57-13.14
RMS Deviations
KeyRefinement Restraint Deviation
c_scangle_it3.217
c_scbond_it2.123
c_mcangle_it1.98
c_mcbond_it1.332
c_angle_deg1.294
c_bond_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1845
Nucleic Acid Atoms
Solvent Atoms115
Heterogen Atoms19

Software

Software
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction