7MGB | pdb_00007mgb

Concanavalin A bound to a DNA glycoconjugate, A(Man-T)AT

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5CNA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	295	Sitting drop comprising 1 uL of Concanavalin A (40 uM) and A(Man-T)AT (160 uM) + 1 uL crystallization condition (Helix screen, condition H10: 0.05 M lithium sulfate, 0.03 M magnesium sulfate heptahydrate, 0.05 M bis Tris (pH 8), 15% w/v PEG 3350). Reservoir contained 70 uL of crystallization condition

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.009	α = 90
b = 117.48	β = 90
c = 122.49	γ = 90

Symmetry
Space Group	P 2 21 21

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 9M		2020-02-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.0782	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.45	84.79	94.87	0.147	0.158	3.9634	7.43		33189

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.45	2.58	99.92		0.83	0.888		7.53

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5CNA	2.45	84.79	33189	1756	94.87	0.2154	0.21304	0.22	0.26221	0.26	RANDOM	34.416

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]
0.52			-4.51		3.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.182
r_dihedral_angle_4_deg	15.776
r_dihedral_angle_3_deg	15.273
r_long_range_B_other	9.256
r_long_range_B_refined	9.254
r_dihedral_angle_1_deg	8.047
r_scangle_other	6.213
r_mcangle_it	5.158
r_mcangle_other	5.158
r_scbond_it	4.003
r_scbond_other	4.002
r_mcbond_it	3.364
r_mcbond_other	3.364
r_angle_refined_deg	1.637
r_angle_other_deg	1.252
r_chiral_restr	0.062
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6793
Nucleic Acid Atoms
Solvent Atoms	103
Heterogen Atoms	60

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing