7Z62 | pdb_00007z62

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	18% PEG3350, 150 mM KSCN, 100 mM Tris/HCl pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.122	α = 90
b = 57.089	β = 90
c = 83.399	γ = 90

Symmetry
Space Group	P 21 21 2

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		2018-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.97918	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	1.53	41.7	99.8	0.0042	0.0047	0.0021	0.999	26.5	9.2		35361			13.4

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	1.53	1.56	99.4		0.264	0.297	0.134	0.987	7.3	9.3

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1OKO	1.53	41.7	35326	1749	99.718	0.168	0.1656	0.18	0.2061	0.22	18.715

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]
1.294			0.739		-2.033

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.781
r_dihedral_angle_3_deg	10.935
r_dihedral_angle_1_deg	6.438
r_dihedral_angle_4_deg	5.663
r_lrange_it	4.748
r_lrange_other	4.538
r_scangle_it	3.417
r_scangle_other	3.416
r_scbond_it	2.409
r_scbond_other	2.408
r_mcangle_other	2.271
r_mcangle_it	2.27
r_angle_refined_deg	1.89
r_mcbond_it	1.693
r_mcbond_other	1.677
r_angle_other_deg	1.572
r_nbd_refined	0.227
r_nbd_other	0.203
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.16
r_xyhbond_nbd_refined	0.147
r_symmetry_nbd_refined	0.146
r_ncsr_local_group_1	0.109
r_chiral_restr	0.096
r_metal_ion_refined	0.093
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.016
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	1797
Nucleic Acid Atoms
Solvent Atoms	390
Heterogen Atoms	38

Software

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