7R55

B-trefoil lectin from Salpingoeca rosetta in complex with Gb3

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	292	0.1 M MOPSO, Bis-Tris pH 6.5, 100 mM amino acids Morpheus I, 35 % PEG SMEAR MEDIUM

Crystal Properties
Matthews coefficient	Solvent content
2.403	48.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.341	α = 90
b = 58.997	β = 90
c = 210.306	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		2021-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.978565	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	1.84	45.18	99.8	0.093	0.106	0.05	0.999	11.8	8.2		62904

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	1.84	1.88			1.034	1.185	0.572	0.792		7.8

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	7QE4	1.84	45.18	62818	2982	99.755	0.187	0.1844	0.2396	27.838

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]
2.658			-1.087		-1.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.779
r_dihedral_angle_4_deg	16.464
r_dihedral_angle_3_deg	13.207
r_dihedral_angle_1_deg	7.599
r_lrange_it	6.748
r_lrange_other	6.673
r_scangle_it	5.544
r_scangle_other	5.544
r_scbond_it	4.148
r_scbond_other	4.148
r_mcangle_it	4.089
r_mcangle_other	4.089
r_mcbond_it	3.214
r_mcbond_other	3.214
r_angle_refined_deg	2.103
r_angle_other_deg	1.487
r_nbd_other	0.231
r_symmetry_xyhbond_nbd_other	0.223
r_symmetry_nbd_refined	0.212
r_nbd_refined	0.199
r_symmetry_nbd_other	0.189
r_symmetry_xyhbond_nbd_refined	0.178
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.171
r_ncsr_local_group_1	0.129
r_chiral_restr	0.102
r_symmetry_nbtor_other	0.086
r_bond_refined_d	0.017
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4956
Nucleic Acid Atoms
Solvent Atoms	604
Heterogen Atoms	140

Software

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