6XIY

Crystal Structure of the Carbohydrate Recognition Domain of the Human Macrophage Galactose C-Type Lectin Bound to methyl 2-(acetylamino)-2-deoxy-1-thio-alpha-D-galactopyranose

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	200mM Magnesium chloride, 2.0 - 2.8M sodium chloride

Crystal Properties
Matthews coefficient	Solvent content
3	58.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.289	α = 90
b = 52.289	β = 90
c = 113.274	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	125	PIXEL	DECTRIS PILATUS3 6M	BE CLR/SI ELLIPTICAL MIRROR	2019-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.9762	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.3	40	99.6	0.191	0.989	14.2	8.9		8370

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.38	99.3		0.899		8.5

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1DV8	2.307	37.787	8348	894	99.654	0.166	0.1618	0.2019	34.941

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]
0.016	0.008		0.016		-0.051

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.179
r_dihedral_angle_3_deg	16.627
r_dihedral_angle_1_deg	11.991
r_dihedral_angle_4_deg	10.862
r_lrange_other	9.99
r_lrange_it	9.974
r_dihedral_angle_other_3_deg	9.947
r_scangle_it	9.389
r_scangle_other	9.383
r_scbond_it	7.098
r_scbond_other	7.092
r_mcangle_it	5.186
r_mcangle_other	5.182
r_mcbond_it	4.508
r_mcbond_other	4.452
r_angle_refined_deg	1.543
r_angle_other_deg	1.332
r_symmetry_nbd_refined	0.215
r_nbd_refined	0.195
r_nbd_other	0.19
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.173
r_metal_ion_refined	0.126
r_symmetry_xyhbond_nbd_refined	0.086
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.074
r_symmetry_xyhbond_nbd_other	0.054
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1047
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing