8RXM | pdb_00008rxm

Galectin-3 in complex with thiogalactoside derivative

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		unpublished structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION		291	30 % PEG 4000, 0.1 M Tris pH 7.5, 0.2 M magnesiumchloride, 0.4 M sodium thiocyanate, 8 mM beta-mercaptoethanol

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.96	α = 90
b = 57.311	β = 90
c = 62.234	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 EIGER X 16M		2020-10-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.8266	MAX IV	BioMAX

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.1	42.16	100	0.047	1	14.9	6.4		53036

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	1.1	1.12			0.899

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	1.1	42.158	52950	2732	99.934	0.107	0.1053	0.1055	0.1298	0.13	13.565

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]
0.37			-0.26		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.279
r_dihedral_angle_3_deg	12.378
r_dihedral_angle_4_deg	10.821
r_dihedral_angle_1_deg	7.726
r_rigid_bond_restr	4.487
r_lrange_it	3.117
r_scangle_it	2.832
r_scangle_other	2.831
r_lrange_other	2.726
r_scbond_it	2.364
r_scbond_other	2.363
r_angle_refined_deg	2.192
r_angle_other_deg	1.537
r_mcangle_other	1.246
r_mcangle_it	1.245
r_mcbond_it	1.099
r_mcbond_other	1.089
r_symmetry_nbd_refined	0.283
r_nbd_refined	0.279
r_nbd_other	0.271
r_symmetry_xyhbond_nbd_refined	0.264
r_xyhbond_nbd_refined	0.194
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.17
r_chiral_restr	0.126
r_symmetry_nbtor_other	0.096
r_bond_refined_d	0.018
r_gen_planes_refined	0.014
r_gen_planes_other	0.006
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1106
Nucleic Acid Atoms
Solvent Atoms	200
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
REFMAC	phasing