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Structural studies on a non-toxic homologue of type II RIPs from Momordica charantia (bitter gourd)-Native-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HWM
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 3.62 66.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.97 α = 90 b = 134.21 β = 90 c = 44.67 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 2009-10-22 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 2.36 29.47 100 0.11 12.2 6 36839 27
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 2.36 2.49 100 3.18 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 1HWM 2.36 29.47 34922 1861 99.9 0.16652 0.16465 0.1733 0.20144 0.2044 RANDOM 28.97
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] 2.47 -1.82 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.982 r_dihedral_angle_4_deg 16.376 r_dihedral_angle_3_deg 13.522 r_dihedral_angle_1_deg 6.671 r_long_range_B_refined 6.009 r_long_range_B_other 6.009 r_scangle_other 4.085 r_mcangle_it 2.878 r_mcangle_other 2.877 r_scbond_it 2.548
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.982 r_dihedral_angle_4_deg 16.376 r_dihedral_angle_3_deg 13.522 r_dihedral_angle_1_deg 6.671 r_long_range_B_refined 6.009 r_long_range_B_other 6.009 r_scangle_other 4.085 r_mcangle_it 2.878 r_mcangle_other 2.877 r_scbond_it 2.548 r_scbond_other 2.548 r_mcbond_it 1.808 r_mcbond_other 1.807 r_angle_refined_deg 1.617 r_angle_other_deg 1.175 r_chiral_restr 0.133 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 3944 Nucleic Acid Atoms Solvent Atoms 407 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement