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Crystal Structure of Mistletoe Lectin I (ML-I) from Viscum album in Complex with 4-N-Furfurylcytosine at 2.84 A Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SZ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 2.5 294 Crystallization 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 coefficient Solvent content 4.08 70
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.677 α = 90 b = 106.677 β = 90 c = 312.569 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2016-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.84 47.5 99.8 17.4 9.6 25725
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1SZ6 2.84 47.5 24367 1272 99.77 0.1663 0.16361 0.1768 0.21812 0.1688 RANDOM 41.475
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] 1 0.5 1 -3.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.462 r_dihedral_angle_4_deg 19.942 r_dihedral_angle_3_deg 15.804 r_long_range_B_refined 9.827 r_long_range_B_other 9.826 r_dihedral_angle_1_deg 8.362 r_scangle_other 6.816 r_mcangle_other 5.747 r_mcangle_it 5.746 r_scbond_it 4.477
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.462 r_dihedral_angle_4_deg 19.942 r_dihedral_angle_3_deg 15.804 r_long_range_B_refined 9.827 r_long_range_B_other 9.826 r_dihedral_angle_1_deg 8.362 r_scangle_other 6.816 r_mcangle_other 5.747 r_mcangle_it 5.746 r_scbond_it 4.477 r_scbond_other 4.476 r_mcbond_it 3.619 r_mcbond_other 3.618 r_angle_refined_deg 2.109 r_angle_other_deg 1.141 r_chiral_restr 0.104 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.002 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 Atoms Number Protein Atoms 3926 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 254
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing