4QC2 | pdb_00004qc2

Crystal structure of lipopolysaccharide transport protein LptB in complex with ATP and Magnesium ions

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JI0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293.25	0.2M ammonium fluoride, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.25K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.16	α = 90
b = 125.76	β = 90
c = 89.61	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	293.25	PIXEL	DECTRIS PILATUS 6M	mirros	2012-05-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.2	44.81	99.9	0.045	0.056	1	4.1	24034	24010	2	1.5	34

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.22	2.29	99.9		0.57	0.6	2	4.3	2362

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	1JI0	2.22	44.81	22834	22804	1230	99.42	0.185	0.18398	0.18067	0.17	0.24825	0.24	RANDOM	45.239

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]
9.13			3.49		-12.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.327
r_dihedral_angle_4_deg	20.728
r_dihedral_angle_3_deg	16.624
r_dihedral_angle_1_deg	6.343
r_angle_refined_deg	1.86
r_chiral_restr	0.125
r_bond_refined_d	0.016
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3658
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms	64

Software

Software
Software Name	Purpose
DNA	data collection
MLPHARE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.