6ELY

Crystal Structure of Mistletoe Lectin I (ML-I) from Viscum album in Complex with 4-N-Furfurylcytosine at 2.84 A Resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SZ6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2.5294Crystallization solution was comprised of ammonium sulphate (30 to 36% w/v), 0.1 M glycine (pH 2.5) and dioxane (4%) in hanging drop vapor diffusion setup. Hexagonal bi-pyramidal crystals were grown within four days.
Crystal Properties
Matthews coefficientSolvent content
4.0870

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.677α = 90
b = 106.677β = 90
c = 312.569γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P111.0332PETRA III, DESYP11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.8447.599.817.49.625725

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 REPLACEMENTTHROUGHOUT1SZ62.8447.524367127299.770.16630.163610.21812RANDOM41.475
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]
10.51-3.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.462
r_dihedral_angle_4_deg19.942
r_dihedral_angle_3_deg15.804
r_long_range_B_refined9.827
r_long_range_B_other9.826
r_dihedral_angle_1_deg8.362
r_scangle_other6.816
r_mcangle_other5.747
r_mcangle_it5.746
r_scbond_it4.477
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.462
r_dihedral_angle_4_deg19.942
r_dihedral_angle_3_deg15.804
r_long_range_B_refined9.827
r_long_range_B_other9.826
r_dihedral_angle_1_deg8.362
r_scangle_other6.816
r_mcangle_other5.747
r_mcangle_it5.746
r_scbond_it4.477
r_scbond_other4.476
r_mcbond_it3.619
r_mcbond_other3.618
r_angle_refined_deg2.109
r_angle_other_deg1.141
r_chiral_restr0.104
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_gen_planes_other0.004
r_bond_other_d0.002
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 Atoms3926
Nucleic Acid Atoms
Solvent Atoms145
Heterogen Atoms254

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing