7MGB

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5CNA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8295Sitting 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 coefficientSolvent content
2.3948.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.009α = 90
b = 117.48β = 90
c = 122.49γ = 90
Symmetry
Space GroupP 2 21 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)Rrim I (All)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
12.4584.7994.870.1470.1583.96347.4333189
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)RedundancyNumber Unique Reflections (All)
12.452.5899.920.830.8887.53

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 REPLACEMENTTHROUGHOUT5CNA2.4584.7933189175694.870.21540.213040.26221RANDOM34.416
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]
0.52-4.513.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.182
r_dihedral_angle_4_deg15.776
r_dihedral_angle_3_deg15.273
r_long_range_B_other9.256
r_long_range_B_refined9.254
r_dihedral_angle_1_deg8.047
r_scangle_other6.213
r_mcangle_it5.158
r_mcangle_other5.158
r_scbond_it4.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.182
r_dihedral_angle_4_deg15.776
r_dihedral_angle_3_deg15.273
r_long_range_B_other9.256
r_long_range_B_refined9.254
r_dihedral_angle_1_deg8.047
r_scangle_other6.213
r_mcangle_it5.158
r_mcangle_other5.158
r_scbond_it4.003
r_scbond_other4.002
r_mcbond_it3.364
r_mcbond_other3.364
r_angle_refined_deg1.637
r_angle_other_deg1.252
r_chiral_restr0.062
r_bond_refined_d0.009
r_gen_planes_refined0.006
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 Atoms6793
Nucleic Acid Atoms
Solvent Atoms103
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing