2Z1V

tRNA guanine transglycosylase E235Q mutant apo structure, pH 8.5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OKOPDB ENTRY 2OKO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52915% PEG 8000, 100mM Tris/HCl pH 8.5, 1mM DTT, 10% DMSO, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.4149.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.757α = 90
b = 65.175β = 96.12
c = 70.455γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113IMAGE PLATERIGAKU RAXIS IV++2006-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU

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
11.552095.60.0580.058162.356093

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 2OKO1.55205309395.60.14430.14260.2032RANDOM
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
728233205.5
RMS Deviations
KeyRefinement Restraint Deviation
s_approx_iso_adps0.072
s_zero_chiral_vol0.053
s_non_zero_chiral_vol0.053
s_similar_adp_cmpnt0.051
s_anti_bump_dis_restr0.029
s_angle_d0.028
s_from_restr_planes0.025
s_bond_d0.01
s_rigid_bond_adp_cmpnt0.003
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2859
Nucleic Acid Atoms
Solvent Atoms305
Heterogen Atoms25

Software

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