2NQZ

Trna-guanine transglycosylase (TGT) mutant in complex with 7-deaza-7-aminomethyl-guanine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Y5X 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5291100mM Tris/HCl, 1mM DTT, 5% PEG 8000, 10% DMSO, 14mg/ml TGT, 20mM preQ1, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3748.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.9α = 90
b = 64.93β = 96.36
c = 71.18γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113IMAGE PLATERIGAKU RAXIS IVmirrors2004-09-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
11.462098.60.044183.26499164991

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 R1Y5X1.46864991649913806492.30.15150.150.150.1984RANDOM
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
3128273365
RMS Deviations
KeyRefinement Restraint Deviation
s_approx_iso_adps0.084
s_zero_chiral_vol0.072
s_non_zero_chiral_vol0.067
s_similar_adp_cmpnt0.051
s_anti_bump_dis_restr0.034
s_angle_d0.031
s_from_restr_planes0.0284
s_bond_d0.011
s_rigid_bond_adp_cmpnt0.004
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2739
Nucleic Acid Atoms
Solvent Atoms258
Heterogen Atoms50

Software

Software
Software NamePurpose
CrystalCleardata collection
CNSrefinement
SHELXLrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing