9SN8 | pdb_00009sn8

Crystal structure of anthocyanin-related glutathione transferase from bilberry

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5F07

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		277	Precipitating solution : - 20% v/v Ethylene glycol / 10 % w/v PEG 8000 - 0,1 M Buffer System 1 pH 6,5 (Buffer System 1 : 1.0M, pH6.5 -> Imidazole; MES monohydrate (acid)) - 0,1 M Amino acids (0.2M DL-Glutamic acid monohydrate; 0.2M DL-Alanine; 0.2M Glycine; 0.2M DL-Lysine monohydrochloride; 0.2M DL-Serine) Protein solution : 14.9 mg/mL protein in 20 mM Tris-HCl pH 8.0 ; 200 mM NaCl ; 1mM EDTA

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.294	α = 90
b = 159.117	β = 95.601
c = 90.374	γ = 90

Symmetry
Space Group	P 1 21 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 4M		2022-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.967697	ESRF	MASSIF-3

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	2.34	89.94	98.8	0.105	0.992	4.8	3.5		65742

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	2.34	2.4	99		0.637	0.612	1.1	3.7

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	2.34	89.94	65706	3282	98.72	0.212	0.2103	0.2103	0.2426	0.2427	48.692

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]
-0.767		-1.228	0.502		0.496

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.848
r_dihedral_angle_6_deg	14.788
r_lrange_it	12.873
r_scangle_it	10.57
r_mcangle_it	8.816
r_scbond_it	7.076
r_dihedral_angle_1_deg	6.339
r_dihedral_angle_2_deg	6.193
r_mcbond_it	5.76
r_angle_refined_deg	1.854
r_nbtor_refined	0.305
r_symmetry_nbd_refined	0.259
r_nbd_refined	0.22
r_symmetry_xyhbond_nbd_refined	0.184
r_xyhbond_nbd_refined	0.14
r_chiral_restr	0.136
r_ncsr_local_group_7	0.08
r_ncsr_local_group_4	0.079
r_ncsr_local_group_5	0.079
r_ncsr_local_group_1	0.076
r_ncsr_local_group_2	0.076
r_ncsr_local_group_3	0.076
r_ncsr_local_group_6	0.076
r_ncsr_local_group_13	0.075
r_ncsr_local_group_9	0.074
r_ncsr_local_group_11	0.074
r_ncsr_local_group_15	0.073
r_ncsr_local_group_14	0.07
r_ncsr_local_group_8	0.069
r_ncsr_local_group_10	0.067
r_ncsr_local_group_12	0.066
r_gen_planes_refined	0.008
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10259
Nucleic Acid Atoms
Solvent Atoms	253
Heterogen Atoms	6

Software

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