8RR9 | pdb_00008rr9

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	1.8 M Ammonium citrate pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.47	α = 90
b = 57.48	β = 90
c = 62.25	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		2022-02-05	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	1.25	42.231	99.5	1.78	0.999	8.9	3.27		65811

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	1.25	1.33			0.066	0.238	0.6

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	31.144	34953	1736	99.903	0.158	0.1567	0.1658	0.1881	0.1926	18.194

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]
2.017			-0.674		-1.343

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.095
r_dihedral_angle_3_deg	11.805
r_lrange_it	11.737
r_lrange_other	11.096
r_scangle_it	7.534
r_scangle_other	7.529
r_dihedral_angle_1_deg	7.356
r_mcangle_it	5.198
r_mcangle_other	5.198
r_scbond_it	5.026
r_scbond_other	5.02
r_dihedral_angle_2_deg	4.905
r_mcbond_it	3.555
r_mcbond_other	3.534
r_rigid_bond_restr	2.452
r_chiral_restr_other	1.676
r_angle_refined_deg	1.475
r_angle_other_deg	0.528
r_nbd_refined	0.198
r_nbd_other	0.197
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.169
r_symmetry_nbd_refined	0.163
r_xyhbond_nbd_refined	0.127
r_symmetry_xyhbond_nbd_refined	0.118
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.067
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1106
Nucleic Acid Atoms
Solvent Atoms	110
Heterogen Atoms	40

Software

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