1PXG

Crystal structure of the mutated tRNA-guanine transglycosylase (TGT) D280E complexed with preQ1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PUDPDB entry 1PUD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5295PEG 8000, dimethylsulfoxide, tris hydrochloride, DTT, preQ1, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.1649.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.28α = 90
b = 64.94β = 96.12
c = 70.2γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray103IMAGE PLATERIGAKU RAXIS IVosmic mirrors2002-11-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.74094.50.0670.06724.33.642492
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7390.60.2530.2536.13.742492

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 REPLACEMENTFREE RPDB entry 1PUD1.71041592395042088930.16070.15940.15940.206RANDOM
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
82736.993169.49
RMS Deviations
KeyRefinement Restraint Deviation
s_similar_adp_cmpnt0.064
s_non_zero_chiral_vol0.053
s_zero_chiral_vol0.047
s_angle_d0.027
s_from_restr_planes0.0234
s_anti_bump_dis_restr0.017
s_bond_d0.008
s_similar_dist
s_rigid_bond_adp_cmpnt
s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2815
Nucleic Acid Atoms
Solvent Atoms290
Heterogen Atoms62

Software

Software
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
SCALEPACKdata scaling
SHELXphasing