2IBT

Crystal structure of the adenine-specific DNA methyltransferase M.TaqI complexed with the cofactor analog AETA and a 10 bp DNA containing 2-aminopurine at the target position and an abasic site analog at the target base partner position


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.32983 microliters crystallization buffer (10mM Tris/HCl, 300mM NaCl, pH 7.3) containing the complex plus 1 microliter reservoir solution (100mM KCl, 100mM MgCl2, 6% isopropanol, 50mM sodium cacodylate, pH 6.0), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1342.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.339α = 90
b = 68.699β = 92.09
c = 114.022γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4mirror2005-05-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-30.9310ESRFID14-3

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
11.719.92980.0770.07711.513.81008439885523.22
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)
11.71.897.30.380.383.653.7615379

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 1G381.719.9210076998855494398.10.16870.16870.166870.20322RANDOM17.313
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]
-0.07-0.070.5-0.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.992
r_dihedral_angle_4_deg15.452
r_dihedral_angle_3_deg13.423
r_dihedral_angle_1_deg6.111
r_scangle_it2.959
r_scbond_it1.946
r_angle_refined_deg1.459
r_mcangle_it1.294
r_mcbond_it0.822
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.992
r_dihedral_angle_4_deg15.452
r_dihedral_angle_3_deg13.423
r_dihedral_angle_1_deg6.111
r_scangle_it2.959
r_scbond_it1.946
r_angle_refined_deg1.459
r_mcangle_it1.294
r_mcbond_it0.822
r_nbtor_refined0.31
r_nbd_refined0.195
r_symmetry_vdw_refined0.162
r_symmetry_hbond_refined0.162
r_xyhbond_nbd_refined0.142
r_chiral_restr0.091
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms6378
Nucleic Acid Atoms792
Solvent Atoms1041
Heterogen Atoms86

Software

Software
Software NamePurpose
REFMACrefinement
ProDCdata collection
MAR345data collection
XDSdata scaling
MOLREPphasing