7OLW | pdb_00007olw

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

X-RAY DIFFRACTION

---

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
1.8	31.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.931	α = 90
b = 42.931	β = 90
c = 94.882	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		2021-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.979	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	1.32	47.44	100	0.054	0.057	0.018	1	30.6	20.2		23283			11.2

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	1.32	1.34	100		0.48	0.505	0.158	0.959	6.7	20.1

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	1.32	37.179	23246	1163	99.996	0.105	0.1032	0.11	0.1293	0.14	14.674

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]
1.987			1.987		-3.974

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.07
r_dihedral_angle_3_deg	11.256
r_dihedral_angle_4_deg	10.751
r_dihedral_angle_1_deg	7.561
r_lrange_it	2.986
r_lrange_other	2.882
r_scangle_it	2.526
r_scangle_other	2.525
r_rigid_bond_restr	2.423
r_scbond_it	2.09
r_scbond_other	2.088
r_mcangle_other	1.878
r_mcangle_it	1.876
r_angle_refined_deg	1.594
r_angle_other_deg	1.544
r_mcbond_it	1.47
r_mcbond_other	1.463
r_nbd_refined	0.206
r_symmetry_nbd_refined	0.206
r_nbd_other	0.198
r_symmetry_nbd_other	0.192
r_xyhbond_nbd_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.178
r_nbtor_refined	0.176
r_symmetry_nbtor_other	0.089
r_symmetry_xyhbond_nbd_other	0.087
r_chiral_restr	0.082
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	987
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms	25

Software

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