Experiment: 9SQT

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OKO

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	291	Buffer Composition (prepared in D2O instead of H2O):16% PEG 6000,1 M LiCl,0.1 M sodium acetate, pD 5 Initial Sitting Drop Setup: Mixed 20 uL of a protein solution containing: 9.6 mg/mL perdeuterated LecA, 5 mM Gal-d10, 5 uM calcium chloride (CaCl2),all dissolved in D2O. With 20 uL of the well solution. Crystal Growth & Feeding Process: Crystals initially appeared after 1 week. To promote further growth, the crystal was fed three times, each time with 5 uL of a pre-equilibrated drop prepared under the same conditions. Each feeding occurred one week apart, starting one week after initial crystal formation. This feeding strategy increased the crystal volume from 0.08 mm3 to 0.74 mm3.

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.29

Symmetry
Space Group	P 1 21 1

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	291	PIXEL	DECTRIS PILATUS 6M		2024-10-07	M	SINGLE WAVELENGTH
2	1	neutron	291	IMAGE PLATE	LADI III		2024-07-08	L	LAUE

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	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	1.49	44.83	98.8	0.09		0.111		0.998		13	5.4		142031
2	1.9	45.9	72.1	0.243	0.206		0.125			6.1	3.1		50313

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.49	1.52		1.688			1.227	0.725		0.9	5.3
2	1.9	2		0.423			0.209			2.4

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1.49	41.52		1.35		141805	3972	98.68		0.1581	0.1572	0.1573	0.1851	0.1849		31.74
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	1.9	45.9				50313		72.1			0.215		0.278

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.8908
f_angle_d	1.6991
f_chiral_restr	0.1135
f_bond_d	0.0138
f_plane_restr	0.0113

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7208
Nucleic Acid Atoms
Solvent Atoms	833
Heterogen Atoms	104

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

9SQT | pdb_00009sqt