8RRA | pdb_00008rra

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	60% "Tacsimate" pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.47	α = 90
b = 57.06	β = 90
c = 60.75	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		2022-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.7999	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	41.59	99.8	0.072	0.998	7.92	3.42		52360

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	1.06	99.7		3.35	0.175	0.4

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	1.3	30.63	31039	1559	99.961	0.166	0.1645	0.1762	0.1968	0.2079	14.986

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]
-1.894			2.673		-0.779

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.981
r_lrange_it	13.359
r_lrange_other	12.124
r_dihedral_angle_3_deg	11.1
r_scangle_it	8.058
r_scangle_other	8.022
r_dihedral_angle_1_deg	7.87
r_dihedral_angle_2_deg	7.077
r_mcangle_it	6.255
r_mcangle_other	6.255
r_rigid_bond_restr	5.899
r_scbond_it	5.789
r_scbond_other	5.758
r_mcbond_it	4.748
r_mcbond_other	4.693
r_angle_refined_deg	1.864
r_chiral_restr_other	1.61
r_angle_other_deg	1.005
r_nbd_refined	0.239
r_symmetry_xyhbond_nbd_refined	0.218
r_symmetry_nbd_other	0.195
r_xyhbond_nbd_refined	0.182
r_nbtor_refined	0.172
r_nbd_other	0.171
r_symmetry_nbd_refined	0.161
r_chiral_restr	0.103
r_symmetry_nbtor_other	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1108
Nucleic Acid Atoms
Solvent Atoms	146
Heterogen Atoms	44

Software

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