2OKO

Z. mobilis tRNA guanine transglycosylase E235Q mutant apo-structure at pH 5.5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Y5XPDB ENTRY 1Y5X

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.5pH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.3349.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.407α = 90
b = 65.194β = 96.36
c = 70.514γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayIMAGE PLATERIGAKU RAXIS IV2006-12-13MSINGLE 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
11.55091.50.12240.032333.5210241

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 1Y5X1.51021024121024185.90.12560.12560.12540.1739RANDOM
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
1928103355.5
RMS Deviations
KeyRefinement Restraint Deviation
s_approx_iso_adps0.081
s_anti_bump_dis_restr0.065
s_zero_chiral_vol0.063
s_non_zero_chiral_vol0.062
s_similar_adp_cmpnt0.054
s_angle_d0.03
s_from_restr_planes0.026
s_bond_d0.011
s_rigid_bond_adp_cmpnt0.004
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2823
Nucleic Acid Atoms
Solvent Atoms346
Heterogen Atoms97

Software

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