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Crystal structure of the complex of Ribosome inactivating protein from Momordica balsamina with Pyrimidine-2,4-dione at 1.70 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ILX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 298 14% PEG 6000, 0.1M Sodium Phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.41 48.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.186 α = 90 b = 130.186 β = 90 c = 39.976 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD MARRESEARCH 2012-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97 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 1.7 65.09 100 0.04 11.3 2 27751
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 1.701 1.745 99.9 2.7
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 5ILX 1.7 65.09 26352 1395 99.99 0.16627 0.16401 0.1751 0.21029 0.2187 RANDOM 25.218
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] -0.7 -0.35 -0.7 2.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.845 r_dihedral_angle_4_deg 19.895 r_dihedral_angle_3_deg 12.553 r_long_range_B_refined 6.374 r_long_range_B_other 6.214 r_dihedral_angle_1_deg 5.809 r_scangle_other 5.014 r_scbond_it 3.44 r_scbond_other 3.439 r_mcangle_it 3.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.845 r_dihedral_angle_4_deg 19.895 r_dihedral_angle_3_deg 12.553 r_long_range_B_refined 6.374 r_long_range_B_other 6.214 r_dihedral_angle_1_deg 5.809 r_scangle_other 5.014 r_scbond_it 3.44 r_scbond_other 3.439 r_mcangle_it 3.079 r_mcangle_other 3.078 r_mcbond_it 2.385 r_mcbond_other 2.377 r_angle_refined_deg 2.007 r_angle_other_deg 1.098 r_chiral_restr 0.121 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.003 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 1910 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing