7QE4

B-trefoil lectin from Salpingoeca rosetta in complex with GalNAc

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	292	0.1 M MOPSO, Bis-Tris pH 6.5, 100 mM AA Morpheus I, 25 % PEG SMEAR MEDIUM

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.158	α = 90
b = 59.254	β = 90
c = 209.612	γ = 90

Symmetry
Space Group	P 21 21 21

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		2020-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.980107	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	1.7	45.19	100	0.078	0.089	0.041	0.999	14.6	8.5		79471

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	1.7	1.73			0.616	0.705	0.339	0.89		8.3

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7QE3	1.7	44.28	79379	3914	99.963	0.171	0.1688	0.2061	19.143

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]
1.285			-0.214		-1.071

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.247
r_dihedral_angle_4_deg	14.054
r_dihedral_angle_3_deg	11.98
r_dihedral_angle_1_deg	7.032
r_lrange_it	4.505
r_lrange_other	4.204
r_scangle_it	2.826
r_scangle_other	2.825
r_scbond_it	1.823
r_scbond_other	1.823
r_mcangle_it	1.766
r_mcangle_other	1.766
r_angle_refined_deg	1.433
r_angle_other_deg	1.369
r_mcbond_it	1.183
r_mcbond_other	1.177
r_symmetry_nbd_refined	0.226
r_nbd_refined	0.193
r_nbd_other	0.188
r_symmetry_xyhbond_nbd_refined	0.184
r_symmetry_nbd_other	0.182
r_xyhbond_nbd_refined	0.166
r_nbtor_refined	0.159
r_ncsr_local_group_1	0.128
r_metal_ion_refined	0.122
r_symmetry_xyhbond_nbd_other	0.098
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.064
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5007
Nucleic Acid Atoms
Solvent Atoms	977
Heterogen Atoms	123

Software

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