7RGZ | pdb_00007rgz

Crystal structure of human galectin-3 CRD in complex with Methyl 2-O-(2-nitro-4-fluoro)-benzoyl-3-O-toluoyl-b-D-talopyranoside

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NMO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	31% PEG 6000, 100mM MgCl2, 8mM beta mercaptoethanol, 100mM Tris-HCL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.258	α = 90
b = 58.22	β = 90
c = 62.723	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	IMAGE PLATE	RIGAKU RAXIS IV++		2016-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.48	42.67	87.9	0.059	14.8	5.6		19942

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.48	1.51			0.389	1.2	1.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	2NMO	1.485	29.127	19892	997	87.983	0.182	0.1799	0.19	0.2151	0.22	17.462

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]
0.005			-0.012		0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.772
r_dihedral_angle_4_deg	11.349
r_dihedral_angle_3_deg	10.597
r_dihedral_angle_1_deg	7.378
r_lrange_it	4.479
r_lrange_other	4.479
r_scangle_it	3.221
r_scangle_other	3.175
r_scbond_it	2.157
r_scbond_other	2.11
r_angle_refined_deg	1.738
r_mcangle_it	1.708
r_mcangle_other	1.708
r_angle_other_deg	1.347
r_mcbond_it	1.25
r_mcbond_other	1.245
r_symmetry_xyhbond_nbd_other	0.232
r_xyhbond_nbd_refined	0.211
r_nbd_refined	0.21
r_symmetry_nbd_other	0.177
r_nbd_other	0.175
r_nbtor_refined	0.164
r_symmetry_xyhbond_nbd_refined	0.128
r_symmetry_nbd_refined	0.093
r_chiral_restr	0.081
r_symmetry_nbtor_other	0.077
r_chiral_restr_other	0.015
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1109
Nucleic Acid Atoms
Solvent Atoms	181
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing