7MG5

Concanavalin A bound to a DNA glycoconjugate, Man-ATAT


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-ATAT (160 uM) + 1 uL crystallization condition (Helix screen, condition D9: 0.05 M bis-Tris (pH 7), 2 M ammonium sulfate, 5% v/v PEG 400). Reservoir contained 70 uL of crystallization condition.
Crystal Properties
Matthews coefficientSolvent content
2.7354.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.689α = 90
b = 70.7β = 90
c = 125.87γ = 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
12.163.0198.30.0697.12337.332700
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)
12.12.2199.90.297.7

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 REPLACEMENTTHROUGHOUT1JBC2.163.0132700169398.30.2030.2010.245RANDOM33.3
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]
-0.081.38-1.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.008
r_dihedral_angle_4_deg18.167
r_dihedral_angle_3_deg13.273
r_dihedral_angle_1_deg8.416
r_long_range_B_refined8.286
r_long_range_B_other8.235
r_scangle_other6.421
r_scbond_it4.18
r_scbond_other4.179
r_mcangle_other4.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.008
r_dihedral_angle_4_deg18.167
r_dihedral_angle_3_deg13.273
r_dihedral_angle_1_deg8.416
r_long_range_B_refined8.286
r_long_range_B_other8.235
r_scangle_other6.421
r_scbond_it4.18
r_scbond_other4.179
r_mcangle_other4.094
r_mcangle_it4.091
r_mcbond_it2.87
r_mcbond_other2.863
r_angle_refined_deg1.54
r_angle_other_deg1.362
r_chiral_restr0.172
r_bond_refined_d0.011
r_gen_planes_refined0.007
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 Atoms3391
Nucleic Acid Atoms164
Solvent Atoms276
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing