3NDI

X-ray Structure of a C-3'-Methyltransferase in Complex with S-adenosylmethionine and dTMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherIn-house MIR model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82981.3 M - 1.5 M Sodium/potassium Phosphate, 10 mM Deoxythymidine 5'-monophosphate, 5 mM S-adenosyl methionine, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3748.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.963α = 90
b = 114.385β = 90
c = 37.782γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135Montel2010-03-24MSINGLE 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
11.550.5960.0840.08410.714.517133868520
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)
1.51.5988.80.350.352.652.5310144

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 REPLACEMENTTHROUGHOUTIn-house MIR model1.5506840964961344896.20.1970.196550.194680.23188RANDOM12.091
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]
-0.22-0.320.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.495
r_dihedral_angle_4_deg17.402
r_dihedral_angle_3_deg13.324
r_dihedral_angle_1_deg6.286
r_scangle_it5.87
r_scbond_it3.97
r_mcangle_it2.604
r_angle_refined_deg2.126
r_mcbond_it1.767
r_chiral_restr0.148
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.495
r_dihedral_angle_4_deg17.402
r_dihedral_angle_3_deg13.324
r_dihedral_angle_1_deg6.286
r_scangle_it5.87
r_scbond_it3.97
r_mcangle_it2.604
r_angle_refined_deg2.126
r_mcbond_it1.767
r_chiral_restr0.148
r_bond_refined_d0.01
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3162
Nucleic Acid Atoms
Solvent Atoms369
Heterogen Atoms59

Software

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