8RR7 | pdb_00008rr7

Galectin-3 with a small molecule inhibitor

X-RAY DIFFRACTION

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	1.8 M Ammonium citrate pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.466	α = 90
b = 57.704	β = 90
c = 62.571	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		2022-01-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.00	SLS	X06DA

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	1.59	30.2	98.4	0.145	0.998	8.9	6.5		17071

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	1.59	1.62			1.03	0.78	2.3

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	1.6	30.2	16839	847	98.583	0.229	0.2277	0.2277	0.2535	0.2535	15.903

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]
-0.171			0.074		0.097

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	10.558
r_dihedral_angle_3_deg	10.407
r_dihedral_angle_1_deg	7.035
r_lrange_it	3.56
r_dihedral_angle_2_deg	2.92
r_scangle_it	1.376
r_angle_refined_deg	1.082
r_mcangle_it	0.879
r_scbond_it	0.824
r_mcbond_it	0.522

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	10.558
r_dihedral_angle_3_deg	10.407
r_dihedral_angle_1_deg	7.035
r_lrange_it	3.56
r_dihedral_angle_2_deg	2.92
r_scangle_it	1.376
r_angle_refined_deg	1.082
r_mcangle_it	0.879
r_scbond_it	0.824
r_mcbond_it	0.522
r_nbtor_refined	0.308
r_nbd_refined	0.181
r_symmetry_nbd_refined	0.168
r_symmetry_xyhbond_nbd_refined	0.16
r_xyhbond_nbd_refined	0.108
r_chiral_restr	0.069
r_gen_planes_refined	0.003
r_bond_refined_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1108
Nucleic Acid Atoms
Solvent Atoms	56
Heterogen Atoms	58

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.