3BLD

tRNA guanine transglycosylase V233G mutant preQ1 complex structure


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BL3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5291100mM Tris/HCl, 1mM DTT, 5% PEG 8000, 10% DMSO, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.2748.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.655α = 90
b = 64.878β = 95.55
c = 70.328γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2007-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.97803BESSY14.2

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
11.198910.041213.7224997116963

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R3bl31.198116963116963910.15120.15080.1854RANDOM
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
1025792925
RMS Deviations
KeyRefinement Restraint Deviation
s_approx_iso_adps0.074
s_zero_chiral_vol0.069
s_non_zero_chiral_vol0.068
s_anti_bump_dis_restr0.053
s_similar_adp_cmpnt0.039
s_angle_d0.028
s_from_restr_planes0.0252
s_bond_d0.012
s_rigid_bond_adp_cmpnt0.005
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2654
Nucleic Acid Atoms
Solvent Atoms250
Heterogen Atoms26

Software

Software
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing