7QE3 | pdb_00007qe3

Se-M variant of 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, HANGING DROP	6.5	292	0.1 M MOPSO, Bis-Tris pH 6.5, 100 mM AA (Arg, Thr, Lys, His), 45 % precipitant mix 6 Morpheus II-2

Crystal Properties
Matthews coefficient	Solvent content
3	59.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.99	α = 90
b = 58.579	β = 90.682
c = 166.424	γ = 90

Symmetry
Space Group	P 1 21 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		2020-10-03	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.9788	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	2.2	39.775	99.5	0.095	0.12	0.072	0.996	11.2	4.9		44177

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	2.2	2.27	98.3		0.503	0.634	0.383	0.852	3	5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	FREE R-VALUE	2.2	39.775	44117	2095	99.403	0.185	0.1824	0.19	0.2312	0.24	31.486

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]
0.042		1.775	-1.792		1.708

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.464
r_dihedral_angle_4_deg	16.772
r_dihedral_angle_3_deg	16.667
r_lrange_it	8.53
r_lrange_other	8.525
r_dihedral_angle_1_deg	7.891
r_scangle_it	6.803
r_scangle_other	6.802
r_mcangle_it	5.201
r_mcangle_other	5.201
r_scbond_it	4.538
r_scbond_other	4.537
r_mcbond_it	3.596
r_mcbond_other	3.595
r_angle_refined_deg	1.92
r_angle_other_deg	1.372
r_symmetry_nbd_refined	0.223
r_nbd_other	0.215
r_nbd_refined	0.196
r_symmetry_nbd_other	0.193
r_xyhbond_nbd_refined	0.172
r_nbtor_refined	0.165
r_symmetry_xyhbond_nbd_refined	0.155
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.085
r_symmetry_xyhbond_nbd_other	0.062
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4983
Nucleic Acid Atoms
Solvent Atoms	450
Heterogen Atoms	71

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
SHELX	model building
SHELX	phasing
CRANK2	phasing
BUCCANEER	model building