4E2X

X-ray Structure of the Y222F mutant of TcaB9, a C-3'-Methyltransferase, in Complex with S-Adenosyl-L-Homocysteine and dTDP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NDJPDB ENTRY 3NDJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82981.2-1.6 M sodium/potassium phosphate, 10 mM dTMP, 5 mM S-adenosyl-L-homocysteine, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3447.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.542α = 90
b = 114.174β = 90
c = 37.632γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135Montel2011-05-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.54178

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
11.43894.70.0720.07210.34.38637481798
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)
11.41.585.20.340.341.831.7413540

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3NDJ1.4388175677644411294.740.206070.204470.23641RANDOM14.959
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]
-0.360.190.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.554
r_dihedral_angle_4_deg20.144
r_dihedral_angle_3_deg13.295
r_scangle_it6.875
r_dihedral_angle_1_deg6.652
r_scbond_it4.375
r_mcangle_it2.853
r_angle_refined_deg2.267
r_mcbond_it1.962
r_chiral_restr0.168
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.554
r_dihedral_angle_4_deg20.144
r_dihedral_angle_3_deg13.295
r_scangle_it6.875
r_dihedral_angle_1_deg6.652
r_scbond_it4.375
r_mcangle_it2.853
r_angle_refined_deg2.267
r_mcbond_it1.962
r_chiral_restr0.168
r_bond_refined_d0.01
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3161
Nucleic Acid Atoms
Solvent Atoms473
Heterogen Atoms68

Software

Software
Software NamePurpose
PROTEUM PLUSdata collection
PHASERphasing
REFMACrefinement
SAINTdata reduction
SADABSdata scaling