8Q5Z | pdb_00008q5z

Crystal structure of bovine Thiosulfate sulfurtransferase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8AGF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	PEG 6000, Tris, calcium chloride dihydrate

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 153.857	α = 90
b = 49.506	β = 98.504
c = 41.863	γ = 90

Symmetry
Space Group	C 1 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		2022-10-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.033220	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.5	38.86	96.2	0.056	0.999	27.9	12.8		47923

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53			0.176	0.989

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	1.5	38.86	47921	2367	95.834	0.147	0.1463	0.16	0.1628	0.17	12.056

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]
-0.253		0.155	0.066		0.134

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.567
r_dihedral_angle_4_deg	14.06
r_dihedral_angle_3_deg	10.34
r_dihedral_angle_1_deg	6.295
r_lrange_it	4.323
r_lrange_other	4.26
r_scangle_it	3.479
r_scangle_other	3.476
r_scbond_it	2.305
r_scbond_other	2.296
r_angle_refined_deg	1.782
r_mcangle_other	1.671
r_mcangle_it	1.669
r_angle_other_deg	1.569
r_mcbond_it	1.124
r_mcbond_other	1.12
r_symmetry_nbd_refined	0.37
r_nbd_other	0.314
r_nbd_refined	0.238
r_nbtor_refined	0.188
r_symmetry_nbd_other	0.177
r_xyhbond_nbd_refined	0.124
r_chiral_restr	0.1
r_symmetry_xyhbond_nbd_refined	0.099
r_metal_ion_refined	0.095
r_symmetry_nbtor_other	0.082
r_bond_refined_d	0.014
r_gen_planes_refined	0.012
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2317
Nucleic Acid Atoms
Solvent Atoms	293
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing