4OQE

Crystal structure of the tylM1 N,N-dimethyltransferase in complex with SAH and TDP-Fuc3NMe


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4OQDPDB ENTRY 4OQD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH929515-20% PEG3400, 200 mM sodium chloride, 5 mM S-adenosylhomocysteine, 10 mM TDP-3-N-methylamino-3,6-dideoxygalactose, pH 9, BATCH, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.5150.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.885α = 90
b = 92.938β = 97.29
c = 77.879γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135Montel2013-05-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
12.25086.50.0570.057143.224812
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)
12.22.371.80.140.143.71.22554

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 4OQD2.229.052481224812125186.50.218640.215330.27695RANDOM37.971
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]
5.444.22-4.11-1.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.314
r_dihedral_angle_4_deg20.863
r_dihedral_angle_3_deg17.354
r_dihedral_angle_1_deg7.52
r_angle_refined_deg1.702
r_angle_other_deg0.84
r_chiral_restr0.088
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.314
r_dihedral_angle_4_deg20.863
r_dihedral_angle_3_deg17.354
r_dihedral_angle_1_deg7.52
r_angle_refined_deg1.702
r_angle_other_deg0.84
r_chiral_restr0.088
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3651
Nucleic Acid Atoms
Solvent Atoms212
Heterogen Atoms124

Software

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