5UDF | pdb_00005udf

Structure of the N-terminal domain of lipoprotein-releasing system transmembrane protein LolE from Acinetobacter baumannii

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	290	Native data set: Microlytic MCSG1 screen H6: 3.5M Sodium formate, 100mM Sodium Acetate / HCl pH 4.6: AcbaC.18885.a.B2.PS02462 at 14.5mg/ml, cryo: 20% EG, tray 265717h6, puck xck3-10. SeMet data set: Microlytic MCSG1 screen H6 optimization: 3M Sodium formate, 100mM Sodium Acetate / HCl pH 4.43: AcbaC.18885.a.B2.PS38034 at 18.0mg/ml, cryo: well D12: 4M Sodium formate, 100mM Sodium Acetate/HCl pH 4.43: tray 265717h6, puck xck3-10

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 156.37	α = 90
b = 156.37	β = 90
c = 91.16	γ = 120

Symmetry
Space Group	H 3

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	RAYONIX MX-300		2016-08-21	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	RAYONIX MX-300		2016-12-16	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
2	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.35	45.14	99.3	0.059	0.998	14.24	3.733		34401		-3	46.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.41	94.7		0.499	0.704	2.29	3.023

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	2.35	45	1.99	34397	2095	99.32	0.179	0.1764	0.18	0.2185	0.22	0	50.8222

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	10.963
f_angle_d	0.82
f_chiral_restr	0.054
f_bond_d	0.006
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5975
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
BUCCANEER	model building
Coot	model building
PHENIX	refinement
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.