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Structural studies on a non-toxic homologue of type II RIPs from Momordica charantia (bitter gourd) in complex with ALPHA-METHYL-D-GALACTOSIDE
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, 20% w/v PEG 10000
Crystal Properties Matthews coefficient Solvent content 2.8 56.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.3 α = 90 b = 136.99 β = 90 c = 44.4 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 2014-03-18 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 2.42 68.5 97.3 0.131 9.2 5.7 25685
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 2.42 2.55 97 1.8 5.3
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 2.42 58.19 24257 1289 96.3 0.224 0.221 0.2521 0.287 0.29 RANDOM 38.07
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] 29.53 -28.37 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.527 r_dihedral_angle_4_deg 16.434 r_dihedral_angle_3_deg 13.33 r_dihedral_angle_1_deg 7.069 r_long_range_B_refined 5.37 r_long_range_B_other 5.344 r_scangle_other 3.507 r_mcangle_it 3.322 r_mcangle_other 3.321 r_scbond_it 2.249
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.527 r_dihedral_angle_4_deg 16.434 r_dihedral_angle_3_deg 13.33 r_dihedral_angle_1_deg 7.069 r_long_range_B_refined 5.37 r_long_range_B_other 5.344 r_scangle_other 3.507 r_mcangle_it 3.322 r_mcangle_other 3.321 r_scbond_it 2.249 r_scbond_other 2.248 r_mcbond_other 2.157 r_mcbond_it 2.156 r_angle_refined_deg 1.468 r_angle_other_deg 1.116 r_chiral_restr 0.131 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 3974 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PHASER phasing MOSFLM data collection