8AGQ

Crystal structure of anthocyanin-related GSTF8 from Populus trichocarpa in complex with (-)-catechin and glutathione

X-RAY DIFFRACTION

---

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, SITTING DROP	6.4	277	1 part protein solution (30mM Tris pH 8, 200mM NaCl, 1mM EDTA) 1 part buffer (100mM MES pH 6.4, 200mM MgCl2, 17.9% PEG200)

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.948	α = 90
b = 55.447	β = 113.55
c = 54.787	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 PILATUS 2M		2020-07-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.999995	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.093	38.496	99.2	0.051	0.055	0.999	15.7	6.4		101092

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.093	1.11			0.608	0.667	0.817	2.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5F07	1.093	38.496	100738	4917	98.833	0.133	0.1324	0.1488	14.844

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]
0.062		0.703	-0.702		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_rigid_bond_restr	24.941
r_dihedral_angle_6_deg	17.525
r_dihedral_angle_3_deg	12.937
r_scbond_it	11.445
r_scbond_other	11.44
r_dihedral_angle_2_deg	8.589
r_scangle_it	7.808
r_scangle_other	7.805
r_lrange_it	6.943
r_lrange_other	6.731
r_dihedral_angle_1_deg	5.997
r_mcangle_it	3.533
r_mcangle_other	3.532
r_mcbond_it	2.808
r_mcbond_other	2.807
r_angle_refined_deg	1.727
r_angle_other_deg	0.626
r_symmetry_nbd_refined	0.377
r_symmetry_xyhbond_nbd_refined	0.331
r_nbd_refined	0.242
r_nbd_other	0.232
r_xyhbond_nbd_refined	0.22
r_nbtor_refined	0.192
r_symmetry_nbd_other	0.189
r_chiral_restr	0.103
r_symmetry_nbtor_other	0.076
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1718
Nucleic Acid Atoms
Solvent Atoms	312
Heterogen Atoms	46

Software

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