4WY2

Crystal structure of universal stress protein E from Proteus mirabilis in complex with UDP-3-O-[(3R)-3-hydroxytetradecanoyl]-N-acetyl-alpha-glucosamine

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	289	0.2 ul of 12 mg/ml protein in 10mM HEPES, 500mM NaCl pH 7.5 were mixed with 0.2 ul of the Quiagen Cryos Suite condition #50 (1.36 M Ammonium Sulfate, 0.085 M MES pH 6.5, 8.5% Dioxane, 15% Glycerol) and equilibrated against the mother liquor in 96 Well 2 drop Crystallization Plate (MRC)

Crystal Properties
Matthews coefficient	Solvent content
3	59.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.877	α = 90
b = 107.877	β = 90
c = 74.923	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD	Beryllium Lenses	2014-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	50	99.6	0.08	0.087	0.033	9.5	6.6		41254		-3	29

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	1.8	1.83	98.7		0.892	0.976	0.389	0.75	1.9	6.1	2017

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	MOLECULAR REPLACEMENT	THROUGHOUT	3OLQ	1.8	50	39066	2019	98.99	0.1736	0.1721	0.2018	RANDOM	35.365

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]
-1.01			-1.01		2.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.567
r_dihedral_angle_4_deg	17.273
r_dihedral_angle_3_deg	13.234
r_dihedral_angle_1_deg	5.457
r_mcangle_it	1.792
r_angle_refined_deg	1.453
r_mcbond_other	1.166
r_mcbond_it	1.165
r_angle_other_deg	0.776
r_chiral_restr	0.086

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.567
r_dihedral_angle_4_deg	17.273
r_dihedral_angle_3_deg	13.234
r_dihedral_angle_1_deg	5.457
r_mcangle_it	1.792
r_angle_refined_deg	1.453
r_mcbond_other	1.166
r_mcbond_it	1.165
r_angle_other_deg	0.776
r_chiral_restr	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2448
Nucleic Acid Atoms
Solvent Atoms	319
Heterogen Atoms	73

Software

Software
Software Name	Purpose
BLU-MAX	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing
REFMAC	refinement
Coot	model building
PDB_EXTRACT	data extraction

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.