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Crystal structure of Ribosome inactivating protein from Momordica balsamina at 1.78 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
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.273 α = 90 b = 130.273 β = 90 c = 40.003 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 2015-09-30 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 1.78 65.14 97.3 0.03 33.8 3.8 23575
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 1.78 1.81 74.5 0.81 2.9
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 1.78 65.14 21711 1168 94.41 0.1646 0.16222 0.1722 0.20684 0.2166 RANDOM 43.584
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] -1.8 -0.9 -1.8 5.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.224 r_dihedral_angle_4_deg 19.414 r_dihedral_angle_3_deg 13.863 r_long_range_B_refined 8.543 r_long_range_B_other 8.506 r_scangle_other 7.047 r_dihedral_angle_1_deg 5.811 r_mcangle_it 4.919 r_mcangle_other 4.917 r_scbond_it 4.751
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.224 r_dihedral_angle_4_deg 19.414 r_dihedral_angle_3_deg 13.863 r_long_range_B_refined 8.543 r_long_range_B_other 8.506 r_scangle_other 7.047 r_dihedral_angle_1_deg 5.811 r_mcangle_it 4.919 r_mcangle_other 4.917 r_scbond_it 4.751 r_scbond_other 4.749 r_mcbond_it 3.686 r_mcbond_other 3.666 r_angle_refined_deg 1.883 r_angle_other_deg 1.042 r_chiral_restr 0.12 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 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 1910 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing