9GF1 | pdb_00009gf1

Cysteine-less human Galectin-3 C173S mutant carbohydrate recognition domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1A3K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	22% (w/v) sodium polyacrylamide 5100, 0.02M magnesium chloride, 0.1M HEPES pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.02	α = 90
b = 58.047	β = 90
c = 63.184	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 EIGER2 X CdTe 16M		2024-06-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.961107	PETRA III, EMBL c/o DESY	P14 (MX2)

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	1.5	58.05	99.8	0.11	0.12	0.045	0.998	9.5	7		22417			10.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53	99.9		0.715		7.1

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	1.5	42.746	22354	1019	99.546	0.162	0.1606	0.1606	0.1859	0.1858	17.507

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]
1.736			-1.096		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.482
r_dihedral_angle_4_deg	12.349
r_dihedral_angle_3_deg	11.365
r_dihedral_angle_1_deg	7.618
r_lrange_it	5.782
r_lrange_other	5.217
r_scangle_it	4.154
r_scangle_other	4.151
r_scbond_it	2.77
r_scbond_other	2.769
r_mcangle_other	1.961
r_mcangle_it	1.96
r_angle_refined_deg	1.763
r_angle_other_deg	1.392
r_mcbond_it	1.368
r_mcbond_other	1.363
r_nbd_refined	0.196
r_xyhbond_nbd_refined	0.171
r_nbtor_refined	0.157
r_symmetry_nbd_other	0.152
r_nbd_other	0.149
r_symmetry_xyhbond_nbd_refined	0.134
r_chiral_restr	0.082
r_symmetry_nbd_refined	0.08
r_symmetry_nbtor_other	0.069
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1108
Nucleic Acid Atoms
Solvent Atoms	149
Heterogen Atoms	32

Software

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