6LZX

Structure of Phytolacca americana UGT3 with 15-crown-5

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PQ6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.2 M Sodium Bromide 20% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.173	α = 90
b = 103.298	β = 90
c = 110.383	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 EIGER X 16M		2018-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

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	3.1	48.73	99.6	0.16	0.17	0.07	0.99	9.7	6.5		19856

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	3.1	3.31	99		0.72	0.78	0.29	0.8		6.9

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	2PQ6	3.101	48.726	19805	967	99.498	0.206	0.2027	0.2598	65.001

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]
-1.757			2.213		-0.455

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.941
r_dihedral_angle_3_deg	19.011
r_dihedral_angle_4_deg	18.531
r_lrange_it	13.341
r_lrange_other	13.341
r_mcangle_other	7.769
r_mcangle_it	7.768
r_scangle_it	7.482
r_scangle_other	7.481
r_dihedral_angle_1_deg	7.049
r_mcbond_it	4.934
r_mcbond_other	4.926
r_scbond_it	4.576
r_scbond_other	4.576
r_angle_other_deg	2.291
r_angle_refined_deg	1.518
r_metal_ion_refined	0.437
r_symmetry_nbd_other	0.222
r_nbd_refined	0.21
r_nbd_other	0.196
r_symmetry_nbd_refined	0.172
r_xyhbond_nbd_refined	0.171
r_nbtor_refined	0.164
r_symmetry_xyhbond_nbd_refined	0.126
r_ncsr_local_group_1	0.114
r_chiral_restr	0.072
r_symmetry_nbtor_other	0.069
r_bond_other_d	0.035
r_ext_dist_refined_d	0.021
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7271
Nucleic Acid Atoms
Solvent Atoms	8
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
BALBES	phasing