6XT6

pro-concanavalin A: Precursor of circularly permuted concanavalin A

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	Zinc chloride, HEPES, PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.939	α = 90
b = 90.42	β = 91.128
c = 86.863	γ = 90

Symmetry
Space Group	I 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	PIXEL	DECTRIS EIGER X 16M		2019-06-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9536	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.1	48.885	98.8	0.994	6.5	3.4		26657

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.16			0.743

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1JBC	2.103	48.885	26647	1307	98.791	0.193	0.1908	0.2441	30.506

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]
1.672		1.335	-2.213		0.488

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.566
r_dihedral_angle_4_deg	19.784
r_dihedral_angle_3_deg	14.399
r_dihedral_angle_1_deg	8.915
r_lrange_it	6.111
r_lrange_other	6.109
r_scangle_it	4.152
r_scangle_other	4.152
r_mcangle_it	3.408
r_mcangle_other	3.407
r_scbond_it	2.742
r_scbond_other	2.741
r_mcbond_it	2.23
r_mcbond_other	2.23
r_angle_refined_deg	1.527
r_angle_other_deg	1.245
r_symmetry_nbd_refined	0.305
r_symmetry_metal_ion_refined	0.262
r_nbd_other	0.255
r_symmetry_xyhbond_nbd_refined	0.237
r_nbd_refined	0.198
r_metal_ion_refined	0.191
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.161
r_xyhbond_nbd_refined	0.126
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.064
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_symmetry_xyhbond_nbd_other	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3677
Nucleic Acid Atoms
Solvent Atoms	80
Heterogen Atoms	68

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
Coot	model building