9I4N | pdb_00009i4n

Galectin-3 in Complex with Methyl 6-fluoro-N-acetyllactosaminide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5ODY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		291	150 mM KBr, 20% PEG MME 2000

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.067	α = 90
b = 58.026	β = 90
c = 63.638	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 2M		2021-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2

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	1.069	42.93	99.2	0.089	0.999	11.85	6.56		116464

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	1.069	1.13	98.1		1.695	0.508	1.06	6.09

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	FOURIER SYNTHESIS	FREE R-VALUE	1.069	42.914	60809	1825	98.915	0.21	0.2091	0.2115	0.2323	0.2343	13.663

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]
0.67			-0.42		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.467
r_dihedral_angle_3_deg	11.765
r_dihedral_angle_1_deg	7.489
r_dihedral_angle_2_deg	6.179
r_lrange_it	4.789
r_lrange_other	4.087
r_scangle_it	2.473
r_scangle_other	2.472
r_angle_refined_deg	1.918
r_scbond_it	1.675
r_scbond_other	1.664
r_mcangle_it	1.437
r_mcangle_other	1.437
r_mcbond_it	1.024
r_mcbond_other	1.018
r_angle_other_deg	0.659
r_nbd_refined	0.309
r_symmetry_nbd_other	0.196
r_nbd_other	0.191
r_nbtor_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.153
r_xyhbond_nbd_refined	0.145
r_symmetry_nbd_refined	0.121
r_chiral_restr	0.103
r_symmetry_nbtor_other	0.091
r_xyhbond_nbd_other	0.037
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1108
Nucleic Acid Atoms
Solvent Atoms	288
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling