1TW9 | pdb_00001tw9

Glutathione Transferase-2, apo form, from the nematode Heligmosomoides polygyrus

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PD2	pdb entry 1PD2 (Prostaglandin D synthase)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	292	PEG 20K, calcium chloride, Tris-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.64	41.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.678	α = 79.09
b = 74.034	β = 80.08
c = 88.573	γ = 81.55

Symmetry
Space Group	P 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 210	Rh-coated Si monochromatic mirrors	2002-10-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1	0.947	CHESS	A1

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	1.7	25	95.9	0.067	12.6	6.2	184048	184048			26.3

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	1.7	1.76	81.4		0.394	2	2.8	15605

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 (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 1PD2 (Prostaglandin D synthase)	1.71	25	184047	179478	4568	95.22	0.18132	0.18002	0.19	0.23198	0.24	RANDOM	29.053

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]
-1.2	0.77	1.04	-0.8	-1.91	2.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.311
r_dihedral_angle_4_deg	17.622
r_dihedral_angle_3_deg	16.876
r_dihedral_angle_1_deg	5.696
r_scangle_it	3.37
r_scbond_it	2.445
r_angle_refined_deg	1.798
r_mcangle_it	1.393
r_mcbond_it	1.095
r_angle_other_deg	1
r_mcbond_other	0.352
r_symmetry_vdw_other	0.296
r_xyhbond_nbd_refined	0.242
r_nbd_refined	0.234
r_symmetry_vdw_refined	0.226
r_symmetry_hbond_refined	0.215
r_nbd_other	0.199
r_chiral_restr	0.144
r_nbtor_other	0.093
r_xyhbond_nbd_other	0.028
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12394
Nucleic Acid Atoms
Solvent Atoms	1860
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
BEAST	phasing