8ZI7 | pdb_00008zi7

Crystal structure of SrUGT76G4 in complex with Rubusoside

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Robetta

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	5.5	293	0.2 M NaSCN, 0.1 M NaCitrate pH5.5, 10-35% PEG3350, 8% D-Sorbitol

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.026	α = 90
b = 77.228	β = 90
c = 86.134	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER2 S 9M		2022-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.97914	SSRF	BL02U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.1	57.5	95.7	0.085	0.093	0.036	0.997	12	6.4		28050

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.22		99.9	0.927	1.001	0.369	0.756		6.9

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.1	57.5	26602	1385	95.56	0.1853	0.1827	0.1916	0.232	0.2346	RANDOM	54.002

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]
1.8			-0.36		-1.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.237
r_long_range_B_other	11.374
r_long_range_B_refined	11.372
r_dihedral_angle_2_deg	8.862
r_scangle_other	8.768
r_dihedral_angle_1_deg	7.003
r_mcangle_other	6.322
r_mcangle_it	6.32
r_scbond_it	5.661
r_scbond_other	5.659
r_mcbond_it	4.447
r_mcbond_other	4.439
r_angle_refined_deg	1.684
r_angle_other_deg	0.565
r_chiral_restr	0.08
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3238
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms	66

Software

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