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Crystal structure Mistletoe Lectin I from Viscum album in complex with kinetin at 2.35 A resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EB2 PDB ENTRY 4EB2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 2.5 293 1.0M ammonium sulphate, 0.2M glycine/HCl, pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 4.6 73.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.01 α = 90 b = 107.01 β = 90 c = 312.42 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 PSI PILATUS 6M 2012-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON OTHER 0.826
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.35 79.7 99.9 0.082 14.09 166806 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.4 99.9 0.013 1.11
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4EB2 2.35 79.7 45113 42857 2256 100 0.22179 0.22039 0.24822 0.2218 RANDOM 51.832
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] 2.03 1.01 2.03 -3.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.378 r_dihedral_angle_4_deg 17.147 r_dihedral_angle_3_deg 13.426 r_dihedral_angle_1_deg 6.073 r_scangle_it 2.444 r_scbond_it 1.382 r_angle_refined_deg 1.32 r_mcangle_it 1.11 r_mcbond_it 0.584 r_chiral_restr 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.378 r_dihedral_angle_4_deg 17.147 r_dihedral_angle_3_deg 13.426 r_dihedral_angle_1_deg 6.073 r_scangle_it 2.444 r_scbond_it 1.382 r_angle_refined_deg 1.32 r_mcangle_it 1.11 r_mcbond_it 0.584 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3945 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 234
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction DNA data collection XDS data reduction MOLREP phasing