2GB4 | pdb_00002gb4

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BZG	pdb entry 2bzg

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP	5.6	293	5.0% 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 coefficient	Solvent content
2.43	48.98

Crystal Data

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

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 325 mm CCD		2005-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2		SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.25	50	79.4	0.033	15.4	2.7		125498

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.25	1.29	46.9		0.325		1.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R	pdb entry 2bzg	1.25	35.9	125430	4154	79.4	0.139	0.136		0.14	0.193	0.19	RANDOM EXPANDED BY TWIN LAW	18.394

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		-0.44	1.96		-1.07

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
11	3551	4169

RMS Deviations
Key	Refinement Restraint Deviation
s_from_restr_planes	0.389
s_approx_iso_adps	0.105
s_similar_dist	0.067
s_zero_chiral_vol	0.065
s_non_zero_chiral_vol	0.063
s_similar_adp_cmpnt	0.04
s_angle_d	0.032
s_anti_bump_dis_restr	0.023
s_bond_d	0.012
s_rigid_bond_adp_cmpnt	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3796
Nucleic Acid Atoms
Solvent Atoms	402
Heterogen Atoms	52

Software

Software
Software Name	Purpose
SHELXL-97	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction
MOLREP	phasing
REFMAC	refinement

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.