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Structural studies on a non-toxic homologue of type II RIPs from Momordica charantia (bitter gourd) in complex with N-acetyl D galactosamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Z8S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 298 0.1 M HEPES, 20% w/v PEG 10000, Glycerol
Crystal Properties Matthews coefficient Solvent content 3.68 66.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.38 α = 90 b = 136.33 β = 90 c = 44.87 γ = 90
Symmetry Space Group P 21 21 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 IMAGE PLATE MAR scanner 345 mm plate 2012-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.53 99.124 98.8 0.181 10.1 6.6 30178 30178
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 2.53 2.67 92.9 0.8 2.2 5.2
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 4Z8S 2.53 60.01 28606 1518 98.76 0.20171 0.19943 0.2035 0.24383 0.2461 RANDOM 23.742
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] 2.11 -1.23 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.727 r_dihedral_angle_4_deg 16.343 r_dihedral_angle_3_deg 13.468 r_dihedral_angle_1_deg 6.633 r_long_range_B_refined 4.794 r_long_range_B_other 4.781 r_scangle_other 3.114 r_angle_other_deg 2.628 r_mcangle_it 2.373 r_mcangle_other 2.373
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.727 r_dihedral_angle_4_deg 16.343 r_dihedral_angle_3_deg 13.468 r_dihedral_angle_1_deg 6.633 r_long_range_B_refined 4.794 r_long_range_B_other 4.781 r_scangle_other 3.114 r_angle_other_deg 2.628 r_mcangle_it 2.373 r_mcangle_other 2.373 r_scbond_it 1.997 r_scbond_other 1.996 r_angle_refined_deg 1.578 r_mcbond_it 1.39 r_mcbond_other 1.39 r_chiral_restr 0.107 r_bond_other_d 0.017 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_gen_planes_other 0.004 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 3974 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 137
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PHASER phasing