8UDB | pdb_00008udb

Crystal Structure of Mu class GST from 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		293	0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.464	α = 90
b = 60.464	β = 90
c = 234.998	γ = 120

Symmetry
Space Group	P 31 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	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	2.75	40	99.7	0.143	0.046	0.989	18	9.5		13765		-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	2.75	2.8	100		0.782	0.273	0.73	2.5	7.8

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	2.75	39.197	13676	714	99.687	0.217	0.2149	0.22	0.2613	0.266	35.729

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]
-1.514	-0.757		-1.514		4.911

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.852
r_dihedral_angle_6_deg	12.524
r_dihedral_angle_2_deg	11.103
r_dihedral_angle_1_deg	5.331
r_lrange_other	5.22
r_lrange_it	5.219
r_scangle_it	2.085
r_scangle_other	2.084
r_mcangle_it	1.673
r_mcangle_other	1.673
r_scbond_it	1.429
r_scbond_other	1.396
r_angle_refined_deg	1.236
r_mcbond_it	0.945
r_mcbond_other	0.945
r_angle_other_deg	0.659
r_nbd_other	0.281
r_symmetry_nbd_other	0.212
r_nbd_refined	0.207
r_nbtor_refined	0.187
r_xyhbond_nbd_refined	0.158
r_ncsr_local_group_1	0.124
r_symmetry_nbd_refined	0.115
r_symmetry_nbtor_other	0.076
r_symmetry_xyhbond_nbd_refined	0.075
r_chiral_restr	0.058
r_bond_refined_d	0.008
r_gen_planes_other	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3600
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms	40

Software

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