8BRO

Structure of the N-terminal domain of BC2L-C lectin (1-131) in complex with a synthetic beta-fucosylamide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6TID

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	292	1.2M Tri sodium citrate ph 7.0

Crystal Properties
Matthews coefficient	Solvent content
1.8	31.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.008	α = 90
b = 43.008	β = 90
c = 94.217	γ = 120

Symmetry
Space Group	P 63

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		2022-09-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.97856	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	1.55	37.25	99.1	0.064	0.076	0.04	0.0998	17.8	5.6		14192

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	1.55	1.58	99.7		0.447	0.54	0.297	0.888	3.5	4.6

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	1.55	37.246	14191	734	98.94	0.144	0.1424	0.1687	10.393

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]
0.147	0.074		0.147		-0.477

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.438
r_dihedral_angle_3_deg	12.328
r_dihedral_angle_1_deg	7.574
r_lrange_it	5.616
r_lrange_other	5.254
r_dihedral_angle_2_deg	4.09
r_scangle_it	3.697
r_scangle_other	3.694
r_scbond_it	2.667
r_scbond_other	2.665
r_mcangle_other	2.286
r_mcangle_it	2.275
r_angle_refined_deg	1.821
r_mcbond_other	1.52
r_mcbond_it	1.516
r_angle_other_deg	0.644
r_nbd_refined	0.208
r_symmetry_nbd_other	0.198
r_symmetry_nbd_refined	0.193
r_nbtor_refined	0.184
r_nbd_other	0.178
r_symmetry_xyhbond_nbd_refined	0.164
r_xyhbond_nbd_refined	0.163
r_chiral_restr	0.103
r_symmetry_nbtor_other	0.091
r_chiral_restr_other	0.088
r_bond_refined_d	0.015
r_gen_planes_refined	0.013
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	955
Nucleic Acid Atoms
Solvent Atoms	122
Heterogen Atoms	26

Software

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