8UDA | pdb_00008uda

Crystal Structure of Mu class Glutathione-S-Transferase, TuGSTm12(Tetur05g05300) from Tetranychus urticae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	SwissModel

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	0.1 M sodium malonate pH 6.0 and 12% w/v polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.34	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.086	α = 90
b = 60.086	β = 90
c = 472.821	γ = 120

Symmetry
Space Group	P 61 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 X 16M		2022-06-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.000	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.8	40	93.8	0.117	0.037	0.997	31.2	10.8		13059		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.87	100		1.012	0.256	0.753	2	15.2

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.8	39.056	12870	664	93.928	0.214	0.2111	0.2158	0.2709	0.2819	107.875

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]
0.314	0.157		0.314		-1.018

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	16.87
r_lrange_it	15.857
r_dihedral_angle_3_deg	13.559
r_dihedral_angle_6_deg	11.009
r_scangle_it	10.322
r_mcangle_it	8.362
r_scbond_it	7.272
r_mcbond_it	5.834
r_dihedral_angle_1_deg	5.536
r_angle_refined_deg	1.283
r_nbtor_refined	0.319
r_nbd_refined	0.224
r_symmetry_nbd_refined	0.198
r_symmetry_xyhbond_nbd_refined	0.134
r_xyhbond_nbd_refined	0.131
r_ncsr_local_group_1	0.12
r_chiral_restr	0.084
r_gen_planes_refined	0.007
r_bond_refined_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3528
Nucleic Acid Atoms
Solvent Atoms	5
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing