2P34

Crystal structure of a lectin from Canavalia maritima seeds (CML) in complex with man1-4man-OMe

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	4.5 - 6.5 sodium formate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.446	α = 90
b = 69.446	β = 90
c = 161.454	γ = 120

Symmetry
Space Group	P 32

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	MAR CCD 130 mm			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE D03B-MX1	1.438	LNLS	D03B-MX1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.1	33.52		0.099	0.099	15.6	5.2		49112

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.1	2.155			0.348	0.39		5.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.1	33.52	46558	2489	96.56	0.17815	0.1749	0.2392	RANDOM	20.194

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.755
r_dihedral_angle_4_deg	20.123
r_dihedral_angle_3_deg	17.22
r_dihedral_angle_1_deg	10.454
r_scangle_it	4.078
r_scbond_it	2.859
r_angle_refined_deg	2.143
r_mcangle_it	1.819
r_mcbond_it	1.065
r_nbtor_refined	0.317

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.755
r_dihedral_angle_4_deg	20.123
r_dihedral_angle_3_deg	17.22
r_dihedral_angle_1_deg	10.454
r_scangle_it	4.078
r_scbond_it	2.859
r_angle_refined_deg	2.143
r_mcangle_it	1.819
r_mcbond_it	1.065
r_nbtor_refined	0.317
r_symmetry_vdw_refined	0.264
r_nbd_refined	0.239
r_symmetry_hbond_refined	0.225
r_xyhbond_nbd_refined	0.201
r_chiral_restr	0.157
r_metal_ion_refined	0.129
r_bond_refined_d	0.02
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7106
Nucleic Acid Atoms
Solvent Atoms	445
Heterogen Atoms	104

Software

Software
Software Name	Purpose
REFMAC	refinement

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.