2IH2

Crystal structure of the adenine-specific DNA methyltransferase M.TaqI complexed with the cofactor analog AETA and a 10 bp DNA containing 5-methylpyrimidin-2(1H)-one at the target base partner position


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.32933 microliters crystallization buffer (10 mM Tris/HCl, 300 mM NaCl, pH 7.3) containing the complex plus 1 microliter reservoir solution (100 mM KCl, 100 mM MgCl2, 6% isopropanol, 50 mM sodium cacodylate, pH 6.0), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthew coefficientSolvent content
2.1542.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.439α = 90
b = 68.875β = 92.27
c = 114.349γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 105ID14-2 (mirror)2003-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.619.6695.80.1170.11711.957.212164511653218.55
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)
11.61.6558.60.340.343.583.9210668

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 1G381.6119.64121568116531582695.860.161950.160220.19508RANDOM14.678
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]
-0.13-0.170.32-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.363
r_dihedral_angle_4_deg14.224
r_dihedral_angle_3_deg12.89
r_dihedral_angle_1_deg6.023
r_scangle_it2.589
r_scbond_it1.69
r_angle_refined_deg1.409
r_mcangle_it1.196
r_mcbond_it0.772
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.363
r_dihedral_angle_4_deg14.224
r_dihedral_angle_3_deg12.89
r_dihedral_angle_1_deg6.023
r_scangle_it2.589
r_scbond_it1.69
r_angle_refined_deg1.409
r_mcangle_it1.196
r_mcbond_it0.772
r_nbtor_refined0.311
r_nbd_refined0.197
r_symmetry_vdw_refined0.149
r_symmetry_hbond_refined0.147
r_xyhbond_nbd_refined0.138
r_chiral_restr0.086
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_symmetry_vdw_other
r_nbd_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_angle_other_deg
r_mcbond_other
r_nbtor_other
r_gen_planes_other
r_bond_other_d
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6378
Nucleic Acid Atoms808
Solvent Atoms1413
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
ProDCdata collection
MAR345data collection
XDSdata scaling
MOLREPphasing