3BBY | pdb_00003bby

Crystal structure of glutathione S-transferase (NP_416804.1) from Escherichia coli K12 at 1.85 A resolution

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	NANODROP, 40.0% 2-ethoxyethanol, 0.05M Ca(OAc)2, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.96	α = 90
b = 69.96	β = 90
c = 92.02	γ = 120

Symmetry
Space Group	P 32 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	100	CCD	ADSC QUANTUM 315		2007-11-01	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	0.9184, 0.9795, 0.9796	ALS	8.2.1

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	1.85	28.772	99.7	0.159	8.16	8.99		22750		-3	16.68

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	1.85	1.92	98		0.791	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	MAD	THROUGHOUT	1.85	28.772	22714	1768	99.94	0.161	0.158	0.17	0.195	0.2	RANDOM	16.365

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]
0.45	0.23		0.45		-0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.816
r_dihedral_angle_4_deg	22.952
r_dihedral_angle_3_deg	12.839
r_scangle_it	6.145
r_dihedral_angle_1_deg	5.519
r_scbond_it	4.549
r_mcangle_it	2.735
r_mcbond_it	1.845
r_angle_refined_deg	1.3
r_angle_other_deg	0.925
r_mcbond_other	0.495
r_symmetry_vdw_other	0.325
r_symmetry_vdw_refined	0.248
r_nbd_refined	0.218
r_nbd_other	0.201
r_symmetry_hbond_refined	0.188
r_nbtor_refined	0.184
r_metal_ion_refined	0.184
r_xyhbond_nbd_refined	0.166
r_nbtor_other	0.086
r_chiral_restr	0.075
r_symmetry_metal_ion_refined	0.036
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1520
Nucleic Acid Atoms
Solvent Atoms	230
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction