6PY1 | pdb_00006py1

Crystal Structure of the Carbohydrate Recognition Domain of the Human Macrophage Galactose C-Type Lectin Bound to GalNAc

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DV8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	100mM Tris pH 6.0 - 7.0, 200mM Magnesium chloride, 2.0 - 2.8M sodium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.825	α = 90
b = 51.825	β = 90
c = 112.855	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 CRL/SI ELLIPTICAL MIRROR	2018-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.9763	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.7	50	100	0.102	0.977	12.4	8.6		20014

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.73			0.867	0.266	1.6	6.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1DV8	1.701	41.74	19973	933	99.905	0.166	0.1654	0.18	0.1883	0.2	RANDOM SELECTION	18.426

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]
0.094	0.047		0.094		-0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.542
r_dihedral_angle_3_deg	13.004
r_dihedral_angle_1_deg	12.857
r_dihedral_angle_other_3_deg	12.684
r_dihedral_angle_4_deg	7.684
r_lrange_it	5.534
r_lrange_other	5.379
r_scangle_it	4.096
r_scangle_other	4.094
r_mcangle_it	2.877
r_mcangle_other	2.875
r_scbond_other	2.805
r_scbond_it	2.801
r_mcbond_it	1.918
r_mcbond_other	1.804
r_angle_refined_deg	1.639
r_angle_other_deg	1.507
r_symmetry_nbd_refined	0.273
r_symmetry_xyhbond_nbd_refined	0.257
r_xyhbond_nbd_refined	0.238
r_nbd_refined	0.226
r_symmetry_nbd_other	0.196
r_nbd_other	0.189
r_nbtor_refined	0.18
r_metal_ion_refined	0.098
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.013
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	1054
Nucleic Acid Atoms
Solvent Atoms	145
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing