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Structural studies on a non-toxic homologue of type II RIPs from Momordica charantia (bitter gourd)-Native-3
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 3.16 61.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.4 α = 90 b = 119.59 β = 90 c = 44.86 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 CCD MARMOSAIC 225 mm CCD 2013-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.95 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.67 32.5 100 0.07 0.07 15.6 6.4 88689 15.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 1.76 100 0.346 0.346 2.2 6.1
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 1.67 32.5 82678 4369 98.2 0.161 0.16 0.1685 0.183 0.1899 RANDOM 20.52
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] 1.51 -1.15 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.402 r_dihedral_angle_4_deg 16.17 r_dihedral_angle_3_deg 10.861 r_dihedral_angle_1_deg 6.518 r_mcangle_it 2.03 r_angle_refined_deg 1.629 r_mcbond_it 1.289 r_mcbond_other 1.288 r_angle_other_deg 1.226 r_chiral_restr 0.157
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.402 r_dihedral_angle_4_deg 16.17 r_dihedral_angle_3_deg 10.861 r_dihedral_angle_1_deg 6.518 r_mcangle_it 2.03 r_angle_refined_deg 1.629 r_mcbond_it 1.289 r_mcbond_other 1.288 r_angle_other_deg 1.226 r_chiral_restr 0.157 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3935 Nucleic Acid Atoms Solvent Atoms 570 Heterogen Atoms 121
Software Software Software Name Purpose REFMAC refinement MOSFLM data collection SCALA data scaling PDB_EXTRACT data extraction