3PFG

X-Ray crystal structure the N,N-dimethyltransferase TylM1 from Streptomyces fradiae in complex with SAM and dTDP-phenol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BXOPDB ENTRY 3BXO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729822% monomethylether poly(ethylene glycol) 5000, 2% isopropanol, 100mM MOPS, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3748.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.079α = 90
b = 41.382β = 121.21
c = 86.637γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135Montell2010-03-08MSINGLE 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
11.34910094.30.0470.04713.73.25569755697
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)
1.3491.4487.50.2130.2132.61.69141

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3BXO1.3491005569752903279494.370.184690.184690.183410.20853RANDOM16.587
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]
-0.46-0.190.51-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.131
r_dihedral_angle_4_deg22.823
r_dihedral_angle_3_deg14.8
r_dihedral_angle_1_deg6.474
r_scangle_it5.464
r_scbond_it3.734
r_mcangle_it2.612
r_angle_refined_deg2.154
r_mcbond_it1.692
r_chiral_restr0.149
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.131
r_dihedral_angle_4_deg22.823
r_dihedral_angle_3_deg14.8
r_dihedral_angle_1_deg6.474
r_scangle_it5.464
r_scbond_it3.734
r_mcangle_it2.612
r_angle_refined_deg2.154
r_mcbond_it1.692
r_chiral_restr0.149
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1836
Nucleic Acid Atoms
Solvent Atoms272
Heterogen Atoms62

Software

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