6LZY

Structure of Phytolacca americana UGT3 with 18-crown-6

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
2.36	47.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.732	α = 90
b = 103.864	β = 90
c = 111.638	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		2018-10-21	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	2.4	49.22	99.8	0.17	0.19	0.07	0.99	11.2	6.6		43272

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	2.4	2.49	99		1.22	1.33	0.52	0.7		6.4

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	2.4	49.217	43210	2119	99.776	0.243	0.2413	0.279	45.553

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]
-0.463			-1.604		2.067

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.287
r_dihedral_angle_4_deg	18.883
r_dihedral_angle_3_deg	17.791
r_lrange_other	11.275
r_lrange_it	11.272
r_dihedral_angle_1_deg	6.482
r_mcangle_it	6.171
r_mcangle_other	6.171
r_scangle_it	5.862
r_scangle_other	5.862
r_mcbond_it	3.929
r_mcbond_other	3.918
r_scbond_it	3.605
r_scbond_other	3.605
r_angle_refined_deg	1.522
r_angle_other_deg	1.278
r_metal_ion_refined	0.25
r_nbd_refined	0.202
r_symmetry_nbd_other	0.183
r_symmetry_nbd_refined	0.166
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.163
r_nbd_other	0.156
r_ncsr_local_group_1	0.104
r_symmetry_xyhbond_nbd_refined	0.096
r_chiral_restr	0.085
r_symmetry_nbtor_other	0.078
r_symmetry_xyhbond_nbd_other	0.029
r_ext_dist_refined_d	0.01
r_bond_refined_d	0.008
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	7278
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms	75

Software

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