7Z63 | pdb_00007z63

Structure of the LecA lectin from Pseudomonas aeruginosa in complex with a biaryl-thiogalactoside

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OKO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	292	LecA was dissolved in 20 mM Tris HCl pH 8.0 and 100 mM NaCl to a concentration of 16.9 mgmL and incubated for 3h at room temperature with 3.8 mM of compound. drops were made using the supernatant after centrifugation at 20000 g for 5 minutes since precipitation was observed and a crystallization solution containing 18% PEG3350, 150 mM potassium thiocyanate (KSCN) and 100 mM Tris HCl pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.26	α = 90
b = 61.932	β = 90
c = 180.008	γ = 90

Symmetry
Space Group	P 21 21 21

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		2020-02-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.97856	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.75	45	100	0.067	0.08	0.043	0.998	16.1	6.3		48775

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.78	99.9		0.291	0.347	0.186	0.976	5.3	6.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	1OKO	1.75	43.131	48697	2506	99.938	0.164	0.1613	0.17	0.2074	0.22	13.085

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]
1.167			0.827		-1.995

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.996
r_dihedral_angle_3_deg	12.109
r_dihedral_angle_1_deg	6.603
r_dihedral_angle_4_deg	5.676
r_lrange_it	4.889
r_lrange_other	4.306
r_scangle_it	3.166
r_scangle_other	3.165
r_scbond_other	2.158
r_scbond_it	2.157
r_mcangle_other	2.118
r_mcangle_it	2.117
r_angle_refined_deg	1.809
r_angle_other_deg	1.57
r_mcbond_it	1.509
r_mcbond_other	1.505
r_nbd_refined	0.199
r_symmetry_nbd_other	0.191
r_nbd_other	0.188
r_symmetry_xyhbond_nbd_refined	0.177
r_nbtor_refined	0.174
r_symmetry_nbd_refined	0.166
r_xyhbond_nbd_refined	0.147
r_metal_ion_refined	0.117
r_chiral_restr	0.094
r_symmetry_nbtor_other	0.086
r_symmetry_xyhbond_nbd_other	0.065
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3602
Nucleic Acid Atoms
Solvent Atoms	833
Heterogen Atoms	133

Software

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