2BZG

Crystal structure of thiopurine S-methyltransferase.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293PROTEIN WAS CRYSTALLIZED IN THE PRESENCE OF 6-MERCAPTOPURINE-9-B, D-RIBOFURANOSIDE (PROTEIN: 6-MP-RIBOFURANOSIDE= 1:10) USING THE HANGING DROP VAPOR DIFFUSION METHOD AT 20C BY MIXING 1.5 UL OF THE PROTEIN SOLUTION WITH 1.5 UL OF THE RESERVOIR SOLUTION CONTAINING 24% PEG3350, 0.2 M KCNS, 0.1 M BISTRIS PROPANE, PH 7.0.
Crystal Properties
Matthews coefficientSolvent content
2.448

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.486α = 90
b = 85.486β = 90
c = 69.362γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2005-07-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-IDAPS17-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
11.5836.39990.0711.87.09677465
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)
11.581.6492.90.274.14.24

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.5860.4133511175698.50.2140.2130.249RANDOM18.45
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.474
r_dihedral_angle_4_deg17.856
r_dihedral_angle_3_deg13.146
r_dihedral_angle_1_deg6.026
r_angle_refined_deg1.384
r_symmetry_hbond_refined0.366
r_nbtor_refined0.309
r_nbd_refined0.202
r_symmetry_vdw_refined0.186
r_xyhbond_nbd_refined0.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.474
r_dihedral_angle_4_deg17.856
r_dihedral_angle_3_deg13.146
r_dihedral_angle_1_deg6.026
r_angle_refined_deg1.384
r_symmetry_hbond_refined0.366
r_nbtor_refined0.309
r_nbd_refined0.202
r_symmetry_vdw_refined0.186
r_xyhbond_nbd_refined0.101
r_chiral_restr0.083
r_bond_refined_d0.02
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1858
Nucleic Acid Atoms
Solvent Atoms231
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling