7MGD

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5295Sitting drop comprising 1 uL of Concanavalin A (32 uM) and T(Man-T)TT (128 uM) + 1 uL crystallization condition (Helix screen, condition B6: 0.1 M sodium chloride, 0.005 M strontium chloride hexahydrate, 0.05 M MES (pH 6.5), 17% w/v PEG 4000). Reservoir contained 70 uL of crystallization condition
Crystal Properties
Matthews coefficientSolvent content
2.4549.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.56α = 90
b = 63.97β = 93.3
c = 126.45γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002020-09-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.979APS21-ID-G

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
12.0560.5391.50.0583.27772.4852751
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)
12.052.1683.40.332.48

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 REPLACEMENTTHROUGHOUT1JBC2.0560.5352751293091.50.2130.210.255RANDOM32.32
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]
-0.32-0.023.98-3.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.867
r_dihedral_angle_3_deg12.549
r_dihedral_angle_4_deg11.22
r_dihedral_angle_1_deg8.243
r_long_range_B_refined6.317
r_long_range_B_other6.281
r_scangle_other4.242
r_mcangle_other4.198
r_mcangle_it4.197
r_scbond_it2.845
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.867
r_dihedral_angle_3_deg12.549
r_dihedral_angle_4_deg11.22
r_dihedral_angle_1_deg8.243
r_long_range_B_refined6.317
r_long_range_B_other6.281
r_scangle_other4.242
r_mcangle_other4.198
r_mcangle_it4.197
r_scbond_it2.845
r_scbond_other2.845
r_mcbond_it2.798
r_mcbond_other2.797
r_angle_refined_deg1.464
r_angle_other_deg1.272
r_chiral_restr0.154
r_bond_refined_d0.007
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 Atoms6894
Nucleic Acid Atoms
Solvent Atoms514
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing