8RRF | pdb_00008rrf

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 unliganded 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
1.94	36.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.48	α = 90
b = 57.32	β = 90
c = 61.64	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		2022-12-30	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	1.15	30.092	98.8	0.061	0.999	9.73	3.37		82842

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	1.15	1.22	95.9		1.7	0.26	0.77

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	1.25	30.092	34480	1720	99.748	0.176	0.1745	0.1853	0.1979	0.2039	15.699

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]
2.733			-2.705		-0.027

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.761
r_dihedral_angle_3_deg	13.003
r_lrange_it	8.525
r_lrange_other	7.893
r_dihedral_angle_1_deg	7.476
r_dihedral_angle_2_deg	5.304
r_scangle_it	3.504
r_scangle_other	3.501
r_mcangle_it	2.857
r_mcangle_other	2.857
r_scbond_it	2.185
r_scbond_other	2.181
r_mcbond_it	1.809
r_mcbond_other	1.801
r_angle_refined_deg	1.625
r_chiral_restr_other	1.466
r_rigid_bond_restr	1.409
r_angle_other_deg	0.5
r_symmetry_nbd_other	0.193
r_nbd_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.165
r_nbtor_refined	0.161
r_nbd_other	0.15
r_symmetry_nbd_refined	0.102
r_xyhbond_nbd_refined	0.095
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.059
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1103
Nucleic Acid Atoms
Solvent Atoms	102
Heterogen Atoms	44

Software

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