9WE5 | pdb_00009we5

UDP-Glucose-bound UgtP with deletion of Pro48-Met91 and insertion of a Ser-Ser-Ser linker

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	0.1 M MES, 5% (w/v) PEG6000

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.12	α = 90
b = 64.08	β = 107.234
c = 110.66	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 EIGER X 4M		2024-05-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-1A	1.018	Photon Factory	BL-1A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.7	50	99.4	0.245	0.989	5.49	3.6		9535

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.7	3.9	98.7		1.153	0.612	1.45	3.55

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	3.7	48.045	9535	477	99.52	0.234	0.23	0.2299	0.3105	0.3249	129.425

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]
-0.653		-0.21	-0.986		1.483

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.262
r_lrange_it	25.224
r_dihedral_angle_3_deg	23.165
r_dihedral_angle_4_deg	15.22
r_scangle_it	13.823
r_mcangle_it	13.335
r_scbond_it	8.14
r_mcbond_it	7.923
r_dihedral_angle_1_deg	7.738
r_angle_refined_deg	1.671
r_nbtor_refined	0.327
r_symmetry_nbd_refined	0.276
r_nbd_refined	0.271
r_xyhbond_nbd_refined	0.19
r_ncsr_local_group_1	0.189
r_chiral_restr	0.132
r_ext_dist_refined_d	0.112
r_symmetry_xyhbond_nbd_refined	0.072
r_gen_planes_refined	0.007
r_bond_refined_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5129
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	72

Software

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