6CAF

High Resolution Structure of Concanavalin B from Jack Bean (Canavalia ensiformis), A Chitinase-like Protein

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	2% saturated ammonium sulfate buffered with Na phosphate at pH 6.5. Room temperature, crystallization in about 1 week. Protein dissolved in 5% NaCl and 0.1 M acetic acid.

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.987	α = 90
b = 79.987	β = 90
c = 101.312	γ = 120

Symmetry
Space Group	P 61

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	173	PIXEL	DECTRIS PILATUS3 R CdTe 300K-W		2016-08-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	0.987	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	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	1.3	101.31	82	0.167	0.158	0.168	0.022	1	50.1	51.5		73116

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.33	18.1		0.85	0.78	0.918	0.331	0.71	3.6	5.5

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	1.3	69.27	69491	3565	81.87	0.09728	0.09574	0.12778	RANDOM	22.91

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]
0.03	0.02		0.03		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	51.038
r_dihedral_angle_2_deg	36.089
r_sphericity_bonded	24.045
r_dihedral_angle_4_deg	23.049
r_dihedral_angle_3_deg	13.081
r_scangle_other	12.951
r_long_range_B_refined	11.774
r_long_range_B_other	11.031
r_scbond_other	10.715
r_scbond_it	10.713
r_rigid_bond_restr	7.58
r_dihedral_angle_1_deg	6.039
r_mcangle_other	3.996
r_mcangle_it	3.973
r_mcbond_it	3.184
r_mcbond_other	3.088
r_angle_refined_deg	1.561
r_angle_other_deg	0.977
r_chiral_restr	0.111
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.004
r_gen_planes_other	0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2298
Nucleic Acid Atoms
Solvent Atoms	344
Heterogen Atoms

Software

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