8QK9

Structure of E. coli LpxH in complex with JEDI-1444

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other	Other		unpublished model from this lab

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	293	Morpheus III - G9 1.2 % Cholic acid derivatives mix 0.1 M Buffer System 2 7.5 Precipitant Mix 1

Crystal Properties
Matthews coefficient	Solvent content
2.86	56.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.309	α = 90
b = 81.178	β = 103.32
c = 32.974	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 EIGER X 16M		2019-04-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.918401	MAX IV	BioMAX

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	1.9	67	99.4	0.999	11.1	7.1		24774

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	1.9	2			0.814

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.9	50.01	23478	1293	99.98	0.17949	0.17771	0.21174	RANDOM	38.524

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]
1.75		1.66	-3.71		1.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.74
r_dihedral_angle_2_deg	9.22
r_long_range_B_refined	7.732
r_long_range_B_other	7.697
r_dihedral_angle_1_deg	6.957
r_scangle_other	5.896
r_mcangle_it	4.467
r_mcangle_other	4.467
r_scbond_it	4.165
r_scbond_other	4.091
r_mcbond_it	3.36
r_mcbond_other	3.358
r_angle_refined_deg	1.527
r_angle_other_deg	0.5
r_chiral_restr	0.087
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
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	1826
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms	42

Software

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