6TIG

Structure of the N terminal domain of Bc2L-C lectin (1-131) in complex with Globo H (H-type 3) antigen

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, HANGING DROP	7	292	Sodium citrate 1.2M

Crystal Properties
Matthews coefficient	Solvent content
1.95	37.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.368	α = 90
b = 42.882	β = 96.007
c = 102.648	γ = 90

Symmetry
Space Group	C 1 2 1

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		2018-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.97857	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	1.9	37.1	97.9	0.077	0.105	0.071	0.995	8.7	3.5		25081			17.8

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	1.9	1.94	97		0.363	0.486	0.32	0.861	2.9	3.5

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6TID	1.9	37.1	25080	1552	97.546	0.169	0.1652	0.2265	24.643

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]
-1.21		0.157	-1.499		2.618

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.577
r_dihedral_angle_4_deg	13.144
r_dihedral_angle_3_deg	12.965
r_dihedral_angle_1_deg	7.986
r_lrange_it	6.575
r_lrange_other	6.483
r_scangle_it	4.77
r_scangle_other	4.77
r_mcangle_it	3.863
r_mcangle_other	3.863
r_scbond_it	3.409
r_scbond_other	3.405
r_mcbond_it	2.944
r_mcbond_other	2.944
r_angle_refined_deg	1.998
r_angle_other_deg	1.491
r_symmetry_xyhbond_nbd_refined	0.248
r_nbd_refined	0.201
r_symmetry_nbd_other	0.192
r_xyhbond_nbd_refined	0.191
r_nbd_other	0.189
r_symmetry_nbd_refined	0.183
r_nbtor_refined	0.176
r_chiral_restr	0.102
r_symmetry_nbtor_other	0.095
r_ncsr_local_group_2	0.073
r_ncsr_local_group_1	0.07
r_ncsr_local_group_3	0.07
r_symmetry_xyhbond_nbd_other	0.033
r_bond_refined_d	0.015
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2951
Nucleic Acid Atoms
Solvent Atoms	287
Heterogen Atoms	163

Software

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