7MG6

Concanavalin A bound to a DNA glycoconjugate, Man-AGCT


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JBC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7295Sitting drop comprising 1 uL of Concanavalin A (40 uM) and Man-AGCT (160 uM) + 1 uL crystallization condition (Helix screen, condition D3: 0.2 M lithium sulfate, 0.05 M bis Tris (pH 7), 20% v/v MPD). Reservoir contained 70 uL of crystallization condition.
Crystal Properties
Matthews coefficientSolvent content
2.7355

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.729α = 90
b = 70.89β = 90
c = 125.839γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2020-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.0782APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.770.8999.60.0982.70658.7561815
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.791000.249.03

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1JBC1.770.8961815334199.60.1780.1770.207RANDOM25.61
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]
1.160.11-1.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.581
r_dihedral_angle_4_deg17.767
r_dihedral_angle_3_deg12.387
r_dihedral_angle_1_deg7.898
r_long_range_B_refined7.499
r_long_range_B_other7.407
r_scangle_other6.099
r_scbond_it3.936
r_scbond_other3.935
r_mcangle_other3.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.581
r_dihedral_angle_4_deg17.767
r_dihedral_angle_3_deg12.387
r_dihedral_angle_1_deg7.898
r_long_range_B_refined7.499
r_long_range_B_other7.407
r_scangle_other6.099
r_scbond_it3.936
r_scbond_other3.935
r_mcangle_other3.14
r_mcangle_it3.139
r_mcbond_it2.208
r_mcbond_other2.196
r_angle_refined_deg1.689
r_angle_other_deg1.516
r_chiral_restr0.17
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms3551
Nucleic Acid Atoms164
Solvent Atoms441
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing