2R19 | pdb_00002r19

Crystal structure of the periplasmic lipopolysaccharide transport protein LptA (YhbN), orthorhombic form

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	PEG 3350, Glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.91	α = 90
b = 58.41	β = 90
c = 149.62	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	ADSC QUANTUM 210		2006-04-16	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315		2006-03-16	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.10000	NSLS	X25
2	SYNCHROTRON	NSLS BEAMLINE X29A	0.97960	NSLS	X29A

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	2.15	50	99.6	0.116	0.061	6.5	6.4	23284	13258	1	1	40.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.15	2.23	100		0.739		6.7	2333

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.16	46.03	12567	12567	691	56.78	0.219	0.219	0.217	0.21	0.271	0.27	RANDOM	40.805

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]
0.14			-0.39		0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.814
r_dihedral_angle_4_deg	25.756
r_dihedral_angle_3_deg	17.14
r_dihedral_angle_1_deg	5.566
r_angle_refined_deg	1.611
r_nbtor_refined	0.316
r_symmetry_vdw_refined	0.267
r_nbd_refined	0.256
r_symmetry_hbond_refined	0.179
r_xyhbond_nbd_refined	0.174

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.814
r_dihedral_angle_4_deg	25.756
r_dihedral_angle_3_deg	17.14
r_dihedral_angle_1_deg	5.566
r_angle_refined_deg	1.611
r_nbtor_refined	0.316
r_symmetry_vdw_refined	0.267
r_nbd_refined	0.256
r_symmetry_hbond_refined	0.179
r_xyhbond_nbd_refined	0.174
r_chiral_restr	0.105
r_bond_refined_d	0.016
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2046
Nucleic Acid Atoms
Solvent Atoms	304
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	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.