8E77

rystal structure of Pcryo_0616, the aminotransferase required to synthesize UDP-N-acetyl-3-amino-D-glucosaminuronic acid (UDP-GlcNAc3NA), incomplete with its external aldimine reaction intermediate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8E75

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	Protein incubated with 5 mM UDP-GlcNAc3NA and 1 mM PLP. Precipitant: 18 - 22% poly(ethylene glycol) 8000, 200 mM LiCl, and 100 mM HEPPS (pH 8.0)

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.708	α = 90
b = 96.336	β = 90
c = 139.467	γ = 90

Symmetry
Space Group	C 2 2 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	Bruker PHOTON II		2019-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	BRUKER D8 QUEST	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	1	50	98.7	0.051	16.9	8.6		205549

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1	1.1	95.9		0.456	2	3.1

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	8e75	1	28.27	195010	10539	98.69	0.1477	0.1462	0.1742	RANDOM	11.418

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]
-0.08			-0.03		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.111
r_dihedral_angle_4_deg	20.988
r_dihedral_angle_3_deg	12.102
r_rigid_bond_restr	11.038
r_dihedral_angle_1_deg	6.223
r_angle_refined_deg	1.629
r_angle_other_deg	1.563
r_chiral_restr	0.089
r_bond_refined_d	0.01
r_gen_planes_refined	0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.111
r_dihedral_angle_4_deg	20.988
r_dihedral_angle_3_deg	12.102
r_rigid_bond_restr	11.038
r_dihedral_angle_1_deg	6.223
r_angle_refined_deg	1.629
r_angle_other_deg	1.563
r_chiral_restr	0.089
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2776
Nucleic Acid Atoms
Solvent Atoms	695
Heterogen Atoms	81

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SAINT	data reduction
SADABS	data scaling
REFMAC	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.