9G3S

LecB from Pseudomonas aeruginosa in complex with a synthetic thiofucoside

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5A3O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293.15	PEG 8000, Tris, ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.488	α = 90
b = 96.951	β = 90
c = 128.68	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		2024-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9760	PETRA III, EMBL c/o DESY	P13 (MX1)

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	1.85	48.69	99.9	0.999	12	13.6		80145

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	1.85	1.95			0.753	2.2

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.85	48.69	80064	3930	99.87	0.187	0.1854	0.2194	24.788

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]
-0.89			-0.558		1.447

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.188
r_dihedral_angle_3_deg	10.587
r_dihedral_angle_1_deg	7.222
r_dihedral_angle_2_deg	6.037
r_lrange_it	4.912
r_lrange_other	4.912
r_scangle_it	4.251
r_scangle_other	4.251
r_scbond_it	2.828
r_scbond_other	2.828
r_mcangle_it	2.473
r_mcangle_other	2.472
r_mcbond_it	1.849
r_mcbond_other	1.849
r_angle_refined_deg	1.477
r_angle_other_deg	0.541
r_nbd_refined	0.227
r_symmetry_nbd_refined	0.212
r_symmetry_nbd_other	0.202
r_symmetry_xyhbond_nbd_other	0.165
r_nbtor_refined	0.164
r_nbd_other	0.154
r_xyhbond_nbd_refined	0.145
r_symmetry_xyhbond_nbd_refined	0.118
r_symmetry_nbtor_other	0.088
r_metal_ion_refined	0.082
r_chiral_restr	0.072
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6596
Nucleic Acid Atoms
Solvent Atoms	192
Heterogen Atoms	312

Software

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