8CRI

Crystal structure of LplA1 in complex with lipoic acid (Listeria monocytogenes)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	200 mM NH4Cl, 2.2 M (NH4)2SO4

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.87	α = 90
b = 72.79	β = 98.04
c = 93.05	γ = 90

Symmetry
Space Group	P 1 21 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		2022-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.1	30	97.1	0.055	10.7	2.9		44270

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	2.1	2.2	98.9		0.66	2.1	3

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	2.1	30	42047	2213	97.11	0.22487	0.22334	0.25145	RANDOM	47.39

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]
2.66		-6.14	-1.41		0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.072
r_dihedral_angle_4_deg	14.634
r_dihedral_angle_3_deg	13.765
r_dihedral_angle_1_deg	6.483
r_long_range_B_refined	2.618
r_long_range_B_other	2.561
r_mcangle_it	1.648
r_mcangle_other	1.647
r_scangle_other	1.348
r_angle_refined_deg	1.155
r_mcbond_it	1.15
r_mcbond_other	1.15
r_angle_other_deg	1.046
r_scbond_it	0.943
r_scbond_other	0.943
r_rigid_bond_restr	0.514
r_chiral_restr	0.036
r_bond_refined_d	0.002
r_bond_other_d	0.002
r_gen_planes_refined	0.002
r_gen_planes_other	0.001
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_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4710
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing