Experiment: 9I4M

Galectin-1 in Complex with Methyl 3'-fluoro-N-acetyllactosaminide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3T2T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		291	0.1M Tris-Cl, pH8, 0.2M lithium sulfate, 30% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.902	α = 90
b = 58.167	β = 90
c = 111.727	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 PILATUS 6M		2021-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	1.79	41.7	98.3	0.134	0.998	8.61	5.69		27650			36.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.79	1.9	95.2		2.293	0.541	0.71	5.89

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.794	41.7	27650	1383	98.31	0.257	0.2605	0.3071	0.3048	42.13

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]
32.4107192			-21.9612345		-10.4494847

RMS Deviations
Key	Refinement Restraint Deviation
s_dihedral_angle_6_deg	14.6574
s_dihedral_angle_3_deg	11.3953
s_dihedral_angle_1_deg	8.0004
s_dihedral_angle_2_deg	3.4793
s_angle_nonh_deg	1.7391
s_nbtor	0.2232
s_nbd	0.2143
s_symmetry_nbd	0.2092
s_hbond_nbd	0.1529
s_symmetry_hbond_nbd	0.1128

RMS Deviations
Key	Refinement Restraint Deviation
s_dihedral_angle_6_deg	14.6574
s_dihedral_angle_3_deg	11.3953
s_dihedral_angle_1_deg	8.0004
s_dihedral_angle_2_deg	3.4793
s_angle_nonh_deg	1.7391
s_nbtor	0.2232
s_nbd	0.2143
s_symmetry_nbd	0.2092
s_hbond_nbd	0.1529
s_symmetry_hbond_nbd	0.1128
s_chiral_restr	0.0764
s_bond_nonh_d	0.0093
s_planes	0.0077

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2062
Nucleic Acid Atoms
Solvent Atoms	87
Heterogen Atoms	65

Software

Software
Software Name	Purpose
Servalcat	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

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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.