7OLN | pdb_00007oln

Structure of the N-terminal domain of BC2L-C lectin (1-131) in complex with Lewis y antigen

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
1.96	37.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.887	α = 90
b = 42.887	β = 90
c = 310.001	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 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	1.92	36.88	100	0.073	0.077	0.026	0.999	23.8	15.6		8958			16.9

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	1.92	1.97	100		0.399	0.424	0.143	0.982	7.3

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	1.92	36.88	8957	429	99.922	0.154	0.152	0.16	0.1934	0.2	27.301

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]
0.066	0.033		0.066		-0.214

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.155
r_dihedral_angle_3_deg	12.893
r_dihedral_angle_4_deg	12.001
r_lrange_it	8.702
r_lrange_other	8.574
r_dihedral_angle_1_deg	7.305
r_scangle_it	6.398
r_scangle_other	6.394
r_mcangle_it	4.528
r_mcangle_other	4.525
r_scbond_it	4.389
r_scbond_other	4.388
r_mcbond_it	3.323
r_mcbond_other	3.321
r_angle_refined_deg	1.973
r_angle_other_deg	1.549
r_chiral_restr	0.431
r_symmetry_xyhbond_nbd_refined	0.23
r_xyhbond_nbd_refined	0.213
r_nbd_other	0.204
r_nbd_refined	0.199
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.177
r_symmetry_nbd_refined	0.147
r_symmetry_nbtor_other	0.093
r_symmetry_xyhbond_nbd_other	0.076
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_xyhbond_nbd_other	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	982
Nucleic Acid Atoms
Solvent Atoms	97
Heterogen Atoms	57

Software

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