8UDD | pdb_00008udd

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
experimental model	PDB	8UDA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.2 M magnesium chloride hexahydrate, 0.1M Tris pH 8.5, and 25% w/v polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.34	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.492	α = 90
b = 69.918	β = 90
c = 118.05	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER X 16M		2021-08-03	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	2.65	40	98.8	0.061	0.023	0.998	29	6.9		14919		-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	2.65	2.71	86.1		0.667	0.297	0.829	1.5	4.2

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	2.65	35.967	14739	706	98.933	0.215	0.2124	0.2134	0.2617	0.2627	82.664

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]
-0.536			-1.105		1.641

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.456
r_dihedral_angle_3_deg	14.225
r_dihedral_angle_6_deg	11.448
r_lrange_other	10.203
r_lrange_it	10.201
r_scangle_it	6.784
r_scangle_other	6.783
r_mcangle_it	6.259
r_mcangle_other	6.258
r_dihedral_angle_1_deg	5.468
r_scbond_it	4.582
r_scbond_other	4.578
r_mcbond_it	4.06
r_mcbond_other	4.056
r_angle_refined_deg	1.319
r_angle_other_deg	0.683
r_nbd_refined	0.232
r_nbd_other	0.218
r_symmetry_nbd_other	0.216
r_symmetry_xyhbond_nbd_refined	0.203
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.139
r_ncsr_local_group_1	0.129
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.067
r_bond_refined_d	0.01
r_gen_planes_other	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3424
Nucleic Acid Atoms
Solvent Atoms	32
Heterogen Atoms	40

Software

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