3ZDV

Crystal structure of the LecB lectin from Pseudomonas aeruginosa in complex with Methyl 6-(2,4,6-trimethylphenylsulfonylamido)-6-deoxy-alpha-D-mannopyranoside

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DCQ	PDB ENTRY 3DCQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		330 MM SODIUM CACODYLATE PH 6.5 200 MM AMMONIUM SULPHATE 30% PEG8K

Crystal Properties
Matthews coefficient	Solvent content
1.89	34.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.53	α = 90
b = 76.98	β = 90
c = 99.66	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 PILATUS 6M	KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS PLUS CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL	2012-09-22	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.41	42.25	99.8	0.07	19.2	7.2		76102		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.41	1.47	98.8		0.65	3.1	7

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3DCQ	1.41	42.24	72296	3805	99.78	0.11614	0.1146	0.14529	RANDOM	13.07

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]
0.14			0.95		-1.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.613
r_dihedral_angle_4_deg	19.432
r_sphericity_free	17.879
r_dihedral_angle_3_deg	9.818
r_rigid_bond_restr	7.724
r_dihedral_angle_1_deg	6.692
r_sphericity_bonded	4.798
r_scbond_it	2.009
r_angle_refined_deg	1.651
r_angle_other_deg	1.475
r_mcangle_it	1.27
r_mcbond_it	1.135
r_mcbond_other	1.135
r_nbd_refined	0.261
r_symmetry_vdw_refined	0.249
r_symmetry_vdw_other	0.216
r_nbd_other	0.204
r_nbtor_refined	0.167
r_xyhbond_nbd_refined	0.115
r_chiral_restr	0.104
r_nbtor_other	0.084
r_metal_ion_refined	0.063
r_symmetry_hbond_refined	0.033
r_bond_refined_d	0.015
r_bond_other_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.006
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3308
Nucleic Acid Atoms
Solvent Atoms	453
Heterogen Atoms	123

Software

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