9G8U | pdb_00009g8u

Structure of the LipA:LipB complex from Acinetobacter baumannii

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	7.5	293	1.5 M ammonium sulfate, 0.1 M Bis-Tris propane (pH 7.5), 5% polyethylene glycol (PEG) 400

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.686	α = 90
b = 133.686	β = 90
c = 139.715	γ = 120

Symmetry
Space Group	P 32 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 2M		2021-09-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	.97718	LNLS	W01B-MX2

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	3.174	48.296	96.2	0.997	5.57	19		23444

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	3.174	3.37	97.4		0.214		4

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3.174	48.296	23444	1966	94.365	0.279	0.2771	0.2784	0.295	0.2986	151.148

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]
3.254	1.627		3.254		-10.556

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	30.002
r_scangle_it	24.384
r_mcangle_it	21.611
r_scbond_it	15.922
r_mcbond_it	13.825
r_dihedral_angle_3_deg	6.592
r_dihedral_angle_6_deg	5.361
r_dihedral_angle_1_deg	3.121
r_angle_refined_deg	1.265
r_dihedral_angle_2_deg	1.222
r_nbtor_refined	0.308
r_nbd_refined	0.256
r_symmetry_nbd_refined	0.199
r_metal_ion_refined	0.198
r_symmetry_xyhbond_nbd_refined	0.136
r_xyhbond_nbd_refined	0.112
r_chiral_restr	0.092
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_ext_dist_refined_b	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4605
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms	2

Software

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