8AIJ | pdb_00008aij

STRUCTURE OF THE LECB LECTIN FROM PSEUDOMONAS AERUGINOSA STRAIN PAO1 IN COMPLEX WITH N-(alpha-L-Fucopyranosyl)benzamide (6)

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	4.4	293.15	24% PEG 8K, 1M LiCl and 100 mM sodium acetate pH = 4.4

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.376	α = 101.809
b = 51.589	β = 99.474
c = 52.604	γ = 115.811

Symmetry
Space Group	P 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 9M	Cryogenically cooled channel cut crystal monochromator, a convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors	2022-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.9801	SOLEIL	PROXIMA 2

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	1.5	40.69	95.5	0.051	0.072	0.051	0.997	12.9	3.4		211861

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	1.5	1.53	92.49		1.53	0.45	0.318	0.881	3.4	3.3

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5A3O	1.5	40.69	61588	7571	95.507	0.142	0.1383	0.14	0.1688	0.17	random selection	15.5

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]
0.341	0.222	-0.038	0.097	0.067	-0.542

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.361
r_dihedral_angle_4_deg	17.432
r_dihedral_angle_3_deg	10.679
r_dihedral_angle_1_deg	7.066
r_lrange_other	4.748
r_lrange_it	4.747
r_scangle_it	3.413
r_scangle_other	3.412
r_scbond_it	2.334
r_scbond_other	2.334
r_mcangle_it	1.907
r_mcangle_other	1.907
r_angle_refined_deg	1.824
r_angle_other_deg	1.609
r_mcbond_it	1.319
r_mcbond_other	1.314
r_nbd_refined	0.252
r_symmetry_nbd_refined	0.219
r_nbd_other	0.213
r_symmetry_nbd_other	0.205
r_symmetry_xyhbond_nbd_refined	0.181
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.161
r_symmetry_xyhbond_nbd_other	0.103
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.087
r_metal_ion_refined	0.068
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3286
Nucleic Acid Atoms
Solvent Atoms	509
Heterogen Atoms	100

Software

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