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Crystal structure of the complex of Ribosome inactivating protein from Momordica balsamina with ribose sugar at 1.90 A resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RL9
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 2.48 50.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.748 α = 90 b = 129.748 β = 90 c = 41.457 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 100 CCD MARRESEARCH MIRROR 2015-11-28 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 1.9 38.89 99.4 0.09 19.8 5.6 20400
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 1.9 1.93 95.2 1.23 4.5
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 3RL9 1.9 38.89 19391 1007 99.38 0.15588 0.1531 0.1634 0.20887 0.2137 RANDOM 34.155
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] -0.27 -0.13 -0.27 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.079 r_dihedral_angle_4_deg 18.173 r_dihedral_angle_3_deg 15.328 r_long_range_B_refined 6.324 r_long_range_B_other 6.322 r_dihedral_angle_1_deg 6.172 r_scangle_other 2.824 r_angle_refined_deg 2.446 r_scbond_it 1.877 r_scbond_other 1.867
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.079 r_dihedral_angle_4_deg 18.173 r_dihedral_angle_3_deg 15.328 r_long_range_B_refined 6.324 r_long_range_B_other 6.322 r_dihedral_angle_1_deg 6.172 r_scangle_other 2.824 r_angle_refined_deg 2.446 r_scbond_it 1.877 r_scbond_other 1.867 r_mcangle_it 1.54 r_mcangle_other 1.54 r_angle_other_deg 1.237 r_mcbond_it 1.111 r_mcbond_other 1.109 r_chiral_restr 0.146 r_bond_refined_d 0.028 r_gen_planes_refined 0.012 r_bond_other_d 0.004 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 1911 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing