9H0Q | pdb_00009h0q

N terminal domain of BC2L-C lectin in complex with N-(beta-L-Fucopyranosyl)-biphenyl-3-carboxamide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WQ4	trimer
experimental model	PDB	6TID	monomer

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		292	17% Peg10K, 100 mM sodium acetate and 100 mM Bis-Tris pH 5.5 cryo in 7.6% Peg10K, 22.5% Peg Smear Low, 45 mM sodium acetate and Bis Tris pH 5.5 and 3 mM PMA127

Crystal Properties
Matthews coefficient	Solvent content
3.4	63.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 169.506	α = 90
b = 169.506	β = 90
c = 344.036	γ = 120

Symmetry
Space Group	H 3 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		2024-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.97856	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	2.55	48.932	100	0.091	0.1	0.041	0.999	18.6	11.6		62109

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	2.55	2.62			0.916	1	0.403	0.831	2.7

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	2.55	48.932	62106	3061	99.969	0.181	0.1791	0.1859	0.2219	0.2266	51.209

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]
0.809	0.404		0.809		-2.623

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.526
r_dihedral_angle_2_deg	15.217
r_dihedral_angle_6_deg	14.188
r_lrange_it	10.179
r_lrange_other	10.17
r_scangle_it	8.692
r_scangle_other	8.691
r_dihedral_angle_1_deg	7.343
r_mcangle_other	7.209
r_mcangle_it	7.208

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.526
r_dihedral_angle_2_deg	15.217
r_dihedral_angle_6_deg	14.188
r_lrange_it	10.179
r_lrange_other	10.17
r_scangle_it	8.692
r_scangle_other	8.691
r_dihedral_angle_1_deg	7.343
r_mcangle_other	7.209
r_mcangle_it	7.208
r_scbond_it	6.816
r_scbond_other	6.816
r_mcbond_it	5.635
r_mcbond_other	5.625
r_angle_refined_deg	1.889
r_angle_other_deg	0.599
r_symmetry_xyhbond_nbd_refined	0.286
r_symmetry_nbd_other	0.215
r_nbd_refined	0.199
r_nbtor_refined	0.188
r_nbd_other	0.165
r_xyhbond_nbd_refined	0.15
r_symmetry_nbd_refined	0.146
r_chiral_restr_other	0.105
r_symmetry_nbtor_other	0.093
r_chiral_restr	0.087
r_ncsr_local_group_14	0.08
r_ncsr_local_group_41	0.077
r_ncsr_local_group_23	0.075
r_ncsr_local_group_26	0.075
r_ncsr_local_group_20	0.074
r_ncsr_local_group_38	0.074
r_ncsr_local_group_36	0.072
r_ncsr_local_group_13	0.071
r_ncsr_local_group_29	0.071
r_ncsr_local_group_42	0.071
r_ncsr_local_group_3	0.07
r_ncsr_local_group_10	0.07
r_ncsr_local_group_6	0.069
r_ncsr_local_group_11	0.069
r_ncsr_local_group_31	0.069
r_ncsr_local_group_43	0.068
r_ncsr_local_group_5	0.067
r_ncsr_local_group_21	0.067
r_ncsr_local_group_24	0.067
r_ncsr_local_group_27	0.067
r_ncsr_local_group_2	0.066
r_ncsr_local_group_34	0.066
r_ncsr_local_group_1	0.065
r_ncsr_local_group_12	0.065
r_ncsr_local_group_22	0.064
r_ncsr_local_group_28	0.063
r_ncsr_local_group_30	0.063
r_ncsr_local_group_8	0.062
r_ncsr_local_group_4	0.061
r_ncsr_local_group_18	0.061
r_ncsr_local_group_35	0.061
r_ncsr_local_group_15	0.06
r_ncsr_local_group_16	0.06
r_ncsr_local_group_37	0.059
r_ncsr_local_group_25	0.057
r_ncsr_local_group_32	0.057
r_ncsr_local_group_33	0.057
r_ncsr_local_group_39	0.057
r_ncsr_local_group_40	0.057
r_ncsr_local_group_45	0.057
r_ncsr_local_group_9	0.056
r_ncsr_local_group_19	0.056
r_ncsr_local_group_44	0.054
r_ncsr_local_group_7	0.052
r_ncsr_local_group_17	0.05
r_symmetry_xyhbond_nbd_other	0.045
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002