2GB4

Crystal structure of Thiopurine methyltransferase (18204406) from Mus musculus at 1.35 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BZGpdb entry 2bzg

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP, NANODROP5.62935.0% Glycerol, 19.0% iso-Propanol, 19.0% PEG-4000, 0.1M Citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4348.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.988α = 90
b = 70.554β = 115.7
c = 72.593γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2005-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-2SSRLBL9-2

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
11.255079.40.03315.42.7125498
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)
1.251.2946.90.3251.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE Rpdb entry 2bzg1.2535.9125430415479.40.1390.1360.193RANDOM EXPANDED BY TWIN LAW18.394
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]
-1.26-0.441.96-1.07
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
1135514169
RMS Deviations
KeyRefinement Restraint Deviation
s_from_restr_planes0.389
s_approx_iso_adps0.105
s_similar_dist0.067
s_zero_chiral_vol0.065
s_non_zero_chiral_vol0.063
s_similar_adp_cmpnt0.04
s_angle_d0.032
s_anti_bump_dis_restr0.023
s_bond_d0.012
s_rigid_bond_adp_cmpnt0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3796
Nucleic Acid Atoms
Solvent Atoms402
Heterogen Atoms52

Software

Software
Software NamePurpose
SHELXL-97refinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
MOLREPphasing
REFMACrefinement