1YDK | pdb_00001ydk

Crystal structure of the I219A mutant of human glutathione transferase A1-1 with S-hexylglutathione

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1K3L	PDB ENTRY 1K3L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	PEG 2000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.53	α = 90
b = 91.472	β = 92.4
c = 51.482	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	113	IMAGE PLATE	RIGAKU RAXIS IV		2004-05-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

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	1.95	20	92.7	0.055		3.1	29853	29853

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)
	1.95	2.02	67.8		0.275		2	2163

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	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	THROUGHOUT	PDB ENTRY 1K3L	1.95	20	29016	29853	1515	90.96	0.205	0.218	0.203	0.22	0.253	0.26	RANDOM	18.528

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]
-0.49		0.52	1.01		-0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.02
r_dihedral_angle_3_deg	14.395
r_dihedral_angle_4_deg	10.477
r_dihedral_angle_1_deg	5.017
r_scangle_it	1.495
r_angle_refined_deg	1.012
r_scbond_it	0.972
r_mcangle_it	0.683
r_mcbond_it	0.42
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.02
r_dihedral_angle_3_deg	14.395
r_dihedral_angle_4_deg	10.477
r_dihedral_angle_1_deg	5.017
r_scangle_it	1.495
r_angle_refined_deg	1.012
r_scbond_it	0.972
r_mcangle_it	0.683
r_mcbond_it	0.42
r_nbtor_refined	0.302
r_nbd_refined	0.184
r_symmetry_vdw_refined	0.121
r_symmetry_hbond_refined	0.117
r_xyhbond_nbd_refined	0.111
r_chiral_restr	0.072
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3453
Nucleic Acid Atoms
Solvent Atoms	409
Heterogen Atoms	52

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

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.