4OIZ

Structure, interactions and evolutionary implications of a domain-swapped lectin dimer from Mycobacterium smegmatis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Native structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	2.0M ammonium citrate tribasic, 0.1M bis-tris propane, 60mM methyl-alpha-mannose, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.51	α = 90
b = 80.86	β = 130.69
c = 100.94	γ = 90

Symmetry
Space Group	C 1 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	100	IMAGE PLATE	MAR scanner 345 mm plate	mirrors	2012-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.54179

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	3.4	40	98.4	0.156	6	3.7		10344

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.4	3.58	98.1		0.43		3.7	1500

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Native structure	3.4	40	9835	494	98.26	0.2443	0.242	0.2882	RANDOM	75.581

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]
-3.23		-4.56	2.52		3.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.345
r_dihedral_angle_3_deg	13.583
r_dihedral_angle_4_deg	10.094
r_dihedral_angle_1_deg	5.076
r_angle_refined_deg	0.786
r_mcangle_it	0.681
r_angle_other_deg	0.663
r_mcbond_it	0.368
r_mcbond_other	0.368
r_chiral_restr	0.052

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.345
r_dihedral_angle_3_deg	13.583
r_dihedral_angle_4_deg	10.094
r_dihedral_angle_1_deg	5.076
r_angle_refined_deg	0.786
r_mcangle_it	0.681
r_angle_other_deg	0.663
r_mcbond_it	0.368
r_mcbond_other	0.368
r_chiral_restr	0.052
r_bond_refined_d	0.004
r_bond_other_d	0.004
r_gen_planes_refined	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3951
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	78

Software

Software
Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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.