9I4O | pdb_00009i4o

Galectin-3 in Complex with Methyl 2'-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	43.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.091	α = 90
b = 58.046	β = 90
c = 63.664	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	0.989	42.93	99.6	0.062	0.999	15.4	6.4		147991			12.1

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	0.989	1.05	97.7		1.161	0.603	1.39	5.8

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	MOLECULAR REPLACEMENT	FREE R-VALUE	0.989	42.93	77282	2319	99.683	0.134	0.1334	0.1362	0.158	0.1603	11.721

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]
1.433			-0.946		-0.486

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.928
r_lrange_it	13.683
r_dihedral_angle_3_deg	11.571
r_lrange_other	10.783
r_dihedral_angle_2_deg	8.032
r_dihedral_angle_1_deg	7.634
r_scangle_it	5.66
r_scangle_other	5.657
r_scbond_it	4.1
r_scbond_other	4.097
r_mcangle_other	3.928
r_mcangle_it	3.923
r_rigid_bond_restr	3.922
r_mcbond_it	2.828
r_mcbond_other	2.802
r_angle_refined_deg	2.029
r_angle_other_deg	0.749
r_nbd_refined	0.225
r_symmetry_nbd_other	0.211
r_nbd_other	0.209
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.138
r_symmetry_nbd_refined	0.138
r_symmetry_xyhbond_nbd_refined	0.138
r_chiral_restr	0.124
r_symmetry_xyhbond_nbd_other	0.107
r_symmetry_nbtor_other	0.09
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_chiral_restr_other	0.008
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	316
Heterogen Atoms	39

Software

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