3EH0 | pdb_00003eh0

Crystal Structure of LpxD from Escherichia coli

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IUA	homology model based on pdb code 2IUA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.4	290	0.1 M MES, 2.0 M (NH4)2SO4, 1% doixane, 1 mM DTT, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 157.95	α = 90
b = 94.17	β = 126.5
c = 103.66	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV		2007-11-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	2.6	50	96.7	0.114	0.168	10.6	3.3	38124	36863	1	1

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)
	2.6	2.74	97.2		0.44	3.1	3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	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	homology model based on pdb code 2IUA	2.6	20	2	2	37053	35182	1871	98.51	0.21689	0.21365	0.2057	0.27911	0.2729	RANDOM	43.271

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]
0.68		-1.18			-2.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.058
r_dihedral_angle_4_deg	18.456
r_dihedral_angle_3_deg	13.652
r_scangle_it	6.471
r_dihedral_angle_1_deg	6.405
r_mcangle_it	4.534
r_scbond_it	4.281
r_mcbond_it	3.352
r_angle_refined_deg	1.49
r_symmetry_vdw_refined	0.452
r_nbtor_refined	0.329
r_symmetry_hbond_refined	0.296
r_nbd_refined	0.248
r_xyhbond_nbd_refined	0.156
r_chiral_restr	0.093
r_bond_refined_d	0.015
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7553
Nucleic Acid Atoms
Solvent Atoms	365
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling