1Y5W

tRNA-guanine Transglycosylase (TGT) in complex with 6-Amino-4-[2-(4-methylphenyl)ethyl]-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1P0D 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5291PEG8000, MES, DMSO, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.449

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.92α = 90
b = 65.25β = 95.98
c = 69.97γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2003-03-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

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
11.582096.40.04221.42.45393053930
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)
11.581.6169.30.2213.61.81939

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT1P0D1.58105291552915268195.20.15850.15730.15730.1963RANDOM
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]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
1227143136.5
RMS Deviations
KeyRefinement Restraint Deviation
s_zero_chiral_vol0.062
s_similar_adp_cmpnt0.062
s_non_zero_chiral_vol0.06
s_angle_d0.03
s_from_restr_planes0.026
s_anti_bump_dis_restr0.023
s_bond_d0.011
s_similar_dist
s_rigid_bond_adp_cmpnt
s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2767
Nucleic Acid Atoms
Solvent Atoms333
Heterogen Atoms37

Software

Software
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
CrystalCleardata reduction
HKL-2000data scaling
SHELXphasing