2IGT

Crystal Structure of the SAM Dependent Methyltransferase from Agrobacterium tumefaciens


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62950.1M sodium acetate 4.6, 3.2M sodium formate, 4% glycerol, 5mM SAM, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.7955.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.941α = 90
b = 145.555β = 90
c = 204.895γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2006-06-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-IDAPS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.8942.8399.80.09911.5117.69983799837
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.891.9698.10.6924.314.39691

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.8942.8389666896661001799.660.165340.165340.162310.19236RANDOM25.174
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]
0.67-1.330.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.01
r_dihedral_angle_4_deg19.075
r_dihedral_angle_3_deg15.066
r_dihedral_angle_1_deg6.65
r_scangle_it3.093
r_scbond_it2.044
r_angle_refined_deg1.396
r_mcangle_it1.291
r_mcbond_it0.874
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.01
r_dihedral_angle_4_deg19.075
r_dihedral_angle_3_deg15.066
r_dihedral_angle_1_deg6.65
r_scangle_it3.093
r_scbond_it2.044
r_angle_refined_deg1.396
r_mcangle_it1.291
r_mcbond_it0.874
r_nbtor_refined0.306
r_symmetry_hbond_refined0.23
r_nbd_refined0.217
r_symmetry_vdw_refined0.203
r_xyhbond_nbd_refined0.174
r_chiral_restr0.099
r_bond_refined_d0.013
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 Atoms7395
Nucleic Acid Atoms
Solvent Atoms940
Heterogen Atoms138

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXCDphasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
MLPHAREphasing
Cootmodel building
ARP/wARPmodel building