6W12 | pdb_00006w12

Crystal Structure of the Carbohydrate Recognition Domain of the Human Macrophage Galactose C-Type Lectin Bound to the Tumor-Associated Tn Antigen

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		291	200mM Magnesium chloride, 100mM Tris, 2-3M NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.155	α = 90
b = 52.155	β = 90
c = 112.667	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	2019-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.9863	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	2	42.2	99.6	0.08	0.99	12.1	5.7		12784

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	2	2.07	98.8		0.28	0.89	5.9	4.9

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	1DV8	2	37.584	12751	633	98.891	0.169	0.1677	0.18	0.1961	0.2	16.964

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]
0.072	0.036		0.072		-0.233

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.925
r_dihedral_angle_3_deg	13.522
r_dihedral_angle_1_deg	11.93
r_dihedral_angle_other_3_deg	9.207
r_lrange_other	8.542
r_lrange_it	8.511
r_scangle_it	8.409
r_scangle_other	8.405
r_dihedral_angle_4_deg	8.237
r_scbond_it	6.102
r_scbond_other	6.098
r_mcangle_other	4.308
r_mcangle_it	4.287
r_mcbond_other	3.283
r_mcbond_it	3.28
r_angle_refined_deg	1.576
r_angle_other_deg	1.431
r_symmetry_metal_ion_refined	0.398
r_nbd_refined	0.25
r_symmetry_nbd_refined	0.234
r_symmetry_xyhbond_nbd_refined	0.211
r_symmetry_nbd_other	0.199
r_nbd_other	0.196
r_nbtor_refined	0.181
r_metal_ion_refined	0.168
r_xyhbond_nbd_refined	0.147
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.077
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
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	104
Heterogen Atoms	33

Software

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