4RH8 | pdb_00004rh8

Crystal structure of the outer membrane lipopolysaccharide transport protein LptE (RlpB) from Escherichia coli in the tetragonal crystal form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4NHR	PDB ENTRY 4NHR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	0.8 M sodium formate, 0.1 M Tris/HOAc pH 8.50, 15% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.46	α = 90
b = 102.46	β = 90
c = 166.84	γ = 90

Symmetry
Space Group	P 41 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		PIXEL	DECTRIS PILATUS 6M		2011-03-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1	NSLS	X25

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	200	100			45813	45803		1.6

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	2.26	99.9		1.57

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4NHR	2.2	87.31	43543	2260	99.97	0.22717	0.22536	0.23	0.26176	0.27	RANDOM	58.837

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]
-0.83			-0.83		1.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.641
r_dihedral_angle_4_deg	20.042
r_dihedral_angle_3_deg	18.416
r_long_range_B_other	12.868
r_long_range_B_refined	12.845
r_scangle_other	10.075
r_dihedral_angle_1_deg	8.151
r_mcangle_other	7.727
r_mcangle_it	7.479
r_scbond_it	6.855
r_scbond_other	6.844
r_mcbond_it	5.168
r_mcbond_other	5.168
r_angle_refined_deg	1.998
r_angle_other_deg	1.6
r_chiral_restr	0.123
r_bond_refined_d	0.018
r_gen_planes_refined	0.011
r_bond_other_d	0.008
r_gen_planes_other	0.006
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4195
Nucleic Acid Atoms
Solvent Atoms	169
Heterogen Atoms	12

Software

Software
Software Name	Purpose
CBASS	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
Aimless	data scaling