8S67 | pdb_00008s67

Galectin-3 with a small molecule inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	2.4M Sodium malonate pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.448	α = 90
b = 56.887	β = 90
c = 61.153	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 XE CdTe 16M		2024-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.886	ESRF	ID23-1

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	1.097	30.708	98	0.129	0.99	8.6	8.8		51801

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	1.1	1.12	79		0.847	0.828	2.8

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	1.097	30.708	51798	2531	98.009	0.137	0.1361	0.1445	0.1535	0.1595	8.235

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]
-0.827			1.144		-0.317

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.376
r_lrange_it	13.785
r_dihedral_angle_3_deg	12.129
r_lrange_other	11.363
r_dihedral_angle_1_deg	7.578
r_dihedral_angle_2_deg	7.033
r_scangle_it	6.628
r_scangle_other	6.593
r_rigid_bond_restr	4.79
r_scbond_it	4.591
r_scbond_other	4.569
r_mcangle_other	4.11
r_mcangle_it	4.106
r_mcbond_it	2.82
r_mcbond_other	2.768
r_angle_refined_deg	1.862
r_angle_other_deg	0.697
r_nbd_refined	0.214
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.174
r_nbd_other	0.142
r_xyhbond_nbd_refined	0.133
r_symmetry_nbd_refined	0.12
r_symmetry_xyhbond_nbd_refined	0.117
r_chiral_restr	0.108
r_symmetry_nbtor_other	0.09
r_chiral_restr_other	0.037
r_bond_refined_d	0.013
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	1103
Nucleic Acid Atoms
Solvent Atoms	175
Heterogen Atoms	38

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing