8RDI | pdb_00008rdi

Crystal structure of UDP-galactose 4-epimerase from Pyrococcus horikoshii containing Y145F mutation and with bound NAD and GDP-L-fucose

X-RAY DIFFRACTION

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	6.2	292	Protein was concentrated in 20 mM MOPS, pH 7, 0.2 mM TCEP to 8-10 mg/ml. Crystallization solution contained 0.2 M NaCl, 0.1 M Na/K phosphate, pH 6.2, 50% PEG 200

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.671	α = 90
b = 169.978	β = 97.08
c = 80.074	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS3 6M		2022-04-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.965459	ESRF	MASSIF-1

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	49.66	99.8	0.212	0.252	0.135	0.981	3.9	3.4		29623

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	3.29		99.8	1.117	1.325	0.706	0.506		3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3.1	49.66	1.36	29578	1484	99.71	0.2233	0.2199	0.2266	0.29	0.2878

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.708
f_angle_d	0.75
f_chiral_restr	0.045
f_plane_restr	0.007
f_bond_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9968
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	328

Software

Software
Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.