7OLU | pdb_00007olu

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

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	292	sodium citrate 1.2M

Crystal Properties
Matthews coefficient	Solvent content
1.87	34.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.954	α = 90
b = 43.954	β = 90
c = 94.138	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 9M		2020-09-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.980	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	1.79	47.07	99.7	0.039	0.041	0.013	1	49.1	20.2		9696			20.9

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	1.79	1.83	95.4		0.228	0.241	0.077	0.99	11.1	17.2

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	2wq4	1.793	38.065	9670	454	99.66	0.142	0.1396	0.15	0.1942	0.2	25.797

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]
-5.611			-5.611		11.222

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.58
r_dihedral_angle_4_deg	19.337
r_dihedral_angle_3_deg	11.879
r_dihedral_angle_1_deg	8.145
r_lrange_it	6.578
r_lrange_other	6.564
r_scangle_it	5.156
r_scangle_other	5.152
r_mcangle_it	4.023
r_mcangle_other	4.021
r_scbond_it	3.64
r_scbond_other	3.638
r_mcbond_it	2.983
r_mcbond_other	2.972
r_angle_refined_deg	1.825
r_angle_other_deg	1.53
r_symmetry_xyhbond_nbd_refined	0.242
r_symmetry_nbd_other	0.202
r_nbd_refined	0.196
r_nbd_other	0.184
r_xyhbond_nbd_refined	0.178
r_nbtor_refined	0.173
r_symmetry_nbd_refined	0.151
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.089
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	978
Nucleic Acid Atoms
Solvent Atoms	99
Heterogen Atoms	23

Software

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