6ZZW | pdb_00006zzw

Structure of the N terminal domain of Bc2L-C lectin (1-131) in complex with Globo H (H-type 3) and CAS No 912569-62-1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6TIG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	292	5.5 mg/ml of protein, 1.2 M sodium citrate, 10 mM ligand at 292 K temperature and cryoprotected with 2.5 M sodium malonate

Crystal Properties
Matthews coefficient	Solvent content
1.95	37.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.459	α = 90
b = 42.912	β = 96.1
c = 103.345	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		2020-02-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.9786	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	37.13	98.8	0.134	0.146	0.055	0.994	10.2	6.9		25522

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	98.1		0.531	0.573	0.214	0.898		7.1

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6tig	1.9	37.13	24288	1224	98.43	0.1836	0.1809	0.19	0.2382	0.24	RANDOM	20.848

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]
-0.95		0.12	-1.31		2.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.078
r_dihedral_angle_3_deg	14.246
r_dihedral_angle_4_deg	10.999
r_dihedral_angle_1_deg	7.103
r_angle_refined_deg	1.84
r_angle_other_deg	1.496
r_chiral_restr	0.093
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.078
r_dihedral_angle_3_deg	14.246
r_dihedral_angle_4_deg	10.999
r_dihedral_angle_1_deg	7.103
r_angle_refined_deg	1.84
r_angle_other_deg	1.496
r_chiral_restr	0.093
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2881
Nucleic Acid Atoms
Solvent Atoms	206
Heterogen Atoms	206

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.