8BXY | pdb_00008bxy

FimH in complex with alpha1,6 core-fucosylated oligomannose-3, crystallized in the trigonal space group

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VCO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	291	1.1 M Lithium sulphate; 0.1 M Tris-HCl pH 9.0; 10 mM nickel chloride

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.056	α = 90
b = 91.056	β = 90
c = 79.578	γ = 120

Symmetry
Space Group	P 31 2 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 16M		2018-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.987	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	1.45	56.076	95.16	0.075	0.077	0.017	0.9996	19.325	20.11		56199			24.99

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	1.45	1.556	21.9		1.837	1.949	0.639	0.615	1.6	16.95

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.45	56.076	56198	1481	82.867	0.155	0.1532	0.15	0.2054	0.2	32.691

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]
0.603	0.301		0.603		-1.955

RMS Deviations
Key	Refinement Restraint Deviation
r_rigid_bond_restr	23.863
r_dihedral_angle_6_deg	17.432
r_scbond_it	16.344
r_scangle_it	13.632
r_dihedral_angle_3_deg	11.962
r_lrange_it	10.166
r_dihedral_angle_1_deg	8.084
r_dihedral_angle_2_deg	5.984
r_mcangle_it	5.584
r_mcbond_it	5.091
r_angle_refined_deg	1.809
r_chiral_restr	0.437
r_nbtor_refined	0.315
r_symmetry_nbd_refined	0.217
r_xyhbond_nbd_refined	0.214
r_nbd_refined	0.196
r_symmetry_xyhbond_nbd_refined	0.159
r_ncsr_local_group_1	0.113
r_metal_ion_refined	0.035
r_bond_refined_d	0.016
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2392
Nucleic Acid Atoms
Solvent Atoms	345
Heterogen Atoms	151

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
PHENIX	model building
autoPROC	data processing
XDS	data reduction
XSCALE	data scaling
PHASER	phasing