9HI1 | pdb_00009hi1

STRUCTURE OF HUMAN UDP-GALACTOSE 4-EPIMERASE IN COMPLEX WITH COMPOUND WBX09

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EK5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	18% PEG 3350 0.2 M Na Malonate

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.147	α = 90
b = 110.205	β = 90
c = 135.411	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 16M		2023-07-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.7098	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	0.95	57.76	99.4	1	76.5	40		415408

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.95	0.97			0.33

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	0.95	57.755	408081	2000	94.531	0.181	0.1811	0.1811	0.189	0.1892	15.018

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]
-0.327			0.286		0.041

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.222
r_dihedral_angle_3_deg	11.31
r_dihedral_angle_2_deg	8.479
r_dihedral_angle_1_deg	5.907
r_lrange_it	4.459
r_scangle_it	3.399
r_scbond_it	2.507
r_angle_refined_deg	2.105
r_mcangle_it	1.921
r_mcbond_it	1.329
r_nbtor_refined	0.316
r_symmetry_nbd_refined	0.217
r_nbd_refined	0.209
r_symmetry_xyhbond_nbd_refined	0.156
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.124
r_ncsr_local_group_1	0.124
r_bond_refined_d	0.012
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5282
Nucleic Acid Atoms
Solvent Atoms	581
Heterogen Atoms	184

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
xia2.multiplex	data scaling
PHASER	phasing