8K57 | pdb_00008k57

Crystal structure of sulfur transferase from Frondihabitans sp. PAMC28461 crystallized in the I21 space group

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		wildtype

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		294	10% w/v PEG 20,000, 20% v/v PEG MME 550, 0.03 M of magnesium chloride and calcium chloride as divalent cations, and 0.1 M MOPS/HEPES-Na pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.47	α = 90
b = 34.76	β = 105.722
c = 93.365	γ = 90

Symmetry
Space Group	I 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 9M		2021-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	0.9794	PAL/PLS	5C (4A)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.38	29.147	99.3	0.99	8.4	3.7		11072

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.38	2.47			0.84

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	2.38	29.147	11071	631	99.167	0.184	0.18	0.18	0.2613	0.27	35.072

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]
0.01		0.035	0.035		-0.056

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.739
r_dihedral_angle_4_deg	17.123
r_dihedral_angle_3_deg	15.955
r_dihedral_angle_1_deg	7.748
r_lrange_it	7.047
r_lrange_other	7.047
r_scangle_it	5.203
r_scangle_other	5.202
r_mcangle_it	4.471
r_mcangle_other	4.469
r_scbond_it	3.45
r_scbond_other	3.449
r_mcbond_it	3.034
r_mcbond_other	3.034
r_angle_refined_deg	1.579
r_angle_other_deg	1.268
r_symmetry_nbd_refined	0.319
r_symmetry_xyhbond_nbd_refined	0.236
r_nbd_refined	0.208
r_nbd_other	0.206
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.155
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.066
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2325
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms

Software

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