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Structural studies on a non-toxic homologue of type II RIPs from Momordica charantia (bitter gourd) in complex with lactose
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 0.1M HEPES, 25% w/v PEG 10000
Crystal Properties Matthews coefficient Solvent content 3.39 63.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.38 α = 90 b = 139.57 β = 90 c = 45.1 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 2012-05-07 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 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 2.55 69.79 97.5 0.2 7 6.7 26759
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.69 93.3 2 4.9
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 2.55 69.79 25385 1340 97.1 0.248 0.246 0.2507 0.292 0.293 RANDOM 31.36
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] 5.18 -3.49 -1.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.426 r_dihedral_angle_4_deg 15.096 r_dihedral_angle_3_deg 12.113 r_dihedral_angle_1_deg 6.339 r_long_range_B_refined 2.792 r_long_range_B_other 2.792 r_angle_refined_deg 1.15 r_mcangle_it 1.12 r_mcangle_other 1.119 r_angle_other_deg 0.948
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.426 r_dihedral_angle_4_deg 15.096 r_dihedral_angle_3_deg 12.113 r_dihedral_angle_1_deg 6.339 r_long_range_B_refined 2.792 r_long_range_B_other 2.792 r_angle_refined_deg 1.15 r_mcangle_it 1.12 r_mcangle_other 1.119 r_angle_other_deg 0.948 r_scangle_other 0.945 r_mcbond_it 0.61 r_mcbond_other 0.61 r_scbond_it 0.536 r_scbond_other 0.536 r_chiral_restr 0.102 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 3970 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 123
Software Software Software Name Purpose REFMAC refinement