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Structural studies on a non-toxic homologue of type II RIPs from Momordica charantia (bitter gourd)-Native-2
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, No-cryo protectant used
Crystal Properties Matthews coefficient Solvent content 3.12 60.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.32 α = 90 b = 120.2 β = 90 c = 44.69 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 2011-04-14 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 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 1.77 139.32 99.5 0.129 10.1 6.7 73778 73778 18.9
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 1.77 1.87 97.7 0.43 4 6
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 1.77 91.18 70097 3609 99.34 0.18129 0.17969 0.1883 0.21207 0.2165 RANDOM 23.547
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] 2.82 -1.8 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.473 r_dihedral_angle_4_deg 18.541 r_dihedral_angle_3_deg 11.202 r_dihedral_angle_1_deg 6.779 r_long_range_B_refined 5.942 r_long_range_B_other 5.262 r_scangle_other 3.159 r_mcangle_it 2.295 r_mcangle_other 2.294 r_scbond_it 2.028
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.473 r_dihedral_angle_4_deg 18.541 r_dihedral_angle_3_deg 11.202 r_dihedral_angle_1_deg 6.779 r_long_range_B_refined 5.942 r_long_range_B_other 5.262 r_scangle_other 3.159 r_mcangle_it 2.295 r_mcangle_other 2.294 r_scbond_it 2.028 r_scbond_other 2.028 r_angle_refined_deg 1.563 r_mcbond_it 1.452 r_mcbond_other 1.452 r_angle_other_deg 1.206 r_chiral_restr 0.154 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3953 Nucleic Acid Atoms Solvent Atoms 542 Heterogen Atoms 135
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PHASER phasing