8S7F | pdb_00008s7f

Crystal structure of Escherichia coli LpxH in complex with EBL-2805

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		an unpublished model from our lab

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	295	3% w/v CHAPS, 3% w/v CHAPSO, 3% w/v Sodium glycocholate hydrate, 3% w/v Taurocholic acid sodium salt hydrate Tris (base); BICINE, pH 8.5 40% v/v Ethylene glycol 20 % w/v PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.563	α = 90
b = 52.271	β = 111.22
c = 86.355	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	PIXEL	DECTRIS PILATUS 6M-F		2019-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91589	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.6	80.5	100	0.999	11.1	8.2		43761

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63			0.753

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.6	80.5	41491	2269	99.96	0.18548	0.1844	0.1948	0.20576	0.2181	RANDOM	15.317

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]
0.09		0.07	0.72		-0.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.574
r_dihedral_angle_1_deg	5.985
r_dihedral_angle_2_deg	5.21
r_long_range_B_refined	3.786
r_long_range_B_other	3.585
r_scangle_other	1.929
r_mcangle_it	1.533
r_mcangle_other	1.533
r_scbond_it	1.199
r_scbond_other	1.195
r_angle_refined_deg	1.041
r_mcbond_it	0.894
r_mcbond_other	0.894
r_angle_other_deg	0.382
r_chiral_restr	0.055
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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	1831
Nucleic Acid Atoms
Solvent Atoms	231
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing