7DF5 | pdb_00007df5

Human Galectin-3 CRD in complex with novel tetrahydropyran-based thiodisaccharide mimic inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7CXA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	0.1M Tris (pH 7.5-8.5), 0.1M MgCl2, 0.4M NaSCN, 28-35% PEG 4000 or PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
1.74	29.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.21	α = 90
b = 57.34	β = 90
c = 62.06	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	CCD	RAYONIX MX300-HS		2017-07-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.969	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.08	42.12	100	0.049	0.054	0.02	0.999	18	6.9		56223

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.08	1.11	99.8		0.82	0.889	0.341	0.764		6.7

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7CXA	1.08	31.3	53291	2860	99.95	0.1405	0.139	0.139	0.1687	0.1682	RANDOM	14.735

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]
-0.14			-0.08		0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.147
r_dihedral_angle_4_deg	12.288
r_dihedral_angle_3_deg	10.688
r_dihedral_angle_1_deg	7.61
r_rigid_bond_restr	5.812
r_angle_refined_deg	2.216
r_angle_other_deg	1.507
r_chiral_restr	0.117
r_bond_refined_d	0.022
r_gen_planes_refined	0.012
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1106
Nucleic Acid Atoms
Solvent Atoms	191
Heterogen Atoms	73

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing