2EX4

Crystal Structure of Human methyltransferase AD-003 in complex with S-adenosyl-L-homocysteine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XTP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9.5300Purified AD-003 was was complexed with S-adenosyl-L-homocysteine (SAH) (Sigma) at 1:5 molar ratio of protein:SAH and crystallized using the hanging drop vapor diffusion method at 20 C by mixing 1.5 l of the protein solution with 1.5 l of the reservoir solution containing 18% PEG 3350, 0.2 M KCl, 0.1 M glycine, pH 9.5., VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
2.1242.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.922α = 105.72
b = 47.367β = 88.18
c = 64.734γ = 115.97
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2005-09-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.7510092.24151441514
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.751.7992.3

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 REPLACEMENTTHROUGHOUT1XTP1.7562.023943339433207191.850.197310.197310.193980.25789RANDOM23.848
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]
-0.8-0.12-0.030.380.10.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.778
r_dihedral_angle_4_deg16.363
r_dihedral_angle_3_deg13.595
r_dihedral_angle_1_deg5.774
r_scangle_it2.985
r_scbond_it1.988
r_angle_refined_deg1.345
r_mcangle_it1.306
r_mcbond_it0.839
r_symmetry_vdw_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.778
r_dihedral_angle_4_deg16.363
r_dihedral_angle_3_deg13.595
r_dihedral_angle_1_deg5.774
r_scangle_it2.985
r_scbond_it1.988
r_angle_refined_deg1.345
r_mcangle_it1.306
r_mcbond_it0.839
r_symmetry_vdw_refined0.306
r_nbtor_refined0.303
r_nbd_refined0.197
r_symmetry_hbond_refined0.165
r_xyhbond_nbd_refined0.141
r_chiral_restr0.091
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3528
Nucleic Acid Atoms
Solvent Atoms555
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing