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Crystal structure of the complex of type 1 Ribosome inactivating protein from Momordica balsamina with Uridine at 1.97 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JTP
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 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.115 α = 90 b = 130.115 β = 90 c = 40.632 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 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 1.98 37.56 100 0.1 18 5.8 17904
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 1.98 2.01 99.9 0.76 1.8
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 4JTP 1.98 37.56 16937 962 99.96 0.16118 0.15816 0.1728 0.21404 0.2207 RANDOM 27.555
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] -0.94 -0.47 -0.94 3.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.2 r_dihedral_angle_4_deg 18.951 r_dihedral_angle_3_deg 13.174 r_long_range_B_refined 6.309 r_long_range_B_other 6.308 r_dihedral_angle_1_deg 5.817 r_scangle_other 4.942 r_scbond_it 3.302 r_scbond_other 3.298 r_mcangle_it 2.961
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.2 r_dihedral_angle_4_deg 18.951 r_dihedral_angle_3_deg 13.174 r_long_range_B_refined 6.309 r_long_range_B_other 6.308 r_dihedral_angle_1_deg 5.817 r_scangle_other 4.942 r_scbond_it 3.302 r_scbond_other 3.298 r_mcangle_it 2.961 r_mcangle_other 2.96 r_mcbond_it 2.124 r_mcbond_other 2.103 r_angle_refined_deg 1.834 r_angle_other_deg 1.006 r_chiral_restr 0.104 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 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 1910 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing