5VWM | pdb_00005vwm

Crystal structure of UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (LpxC) from Pseudomonas aeruginosa in complex with CHIR-090 inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3UHM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.7	290	tray289953 G9:HEPES, 100 mM HCl, pH 7.7, 50 mM CaCl, 4% (w/v) Propanol, 25% (w/v) PEG 3350 +1mM ZnCl2, 1mM Chir-090 : Cryo = 20%EG : PsaeA.00166.a.DG15.PD00471 at 5 mg/ml, puck SHD-3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.85	α = 111.3
b = 47.59	β = 109
c = 48.41	γ = 98.39

Symmetry
Space Group	P 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	IMAGE PLATE	RIGAKU RAXIS	mirrors	2017-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X8C	0.97872	NSLS	X8C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.8	42.297	93.9	0.052	0.059	0.998	18.56	4.035		23497		-3	10.48

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.85	83.3		0.182	0.225	0.95	5.02	2.734

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	3uhm	1.8	42.297	1.99	23488	2033	94.27	0.1418	0.1382	0.14	0.1785	0.18	13.4029

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	18.963
f_angle_d	0.848
f_chiral_restr	0.056
f_bond_d	0.006
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2335
Nucleic Acid Atoms
Solvent Atoms	369
Heterogen Atoms	47

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

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.