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Crystal structure of Ribosome inactivating protein from Momordica balsamina with Uracil at 1.70 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FPZ
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 2.37 48
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 37.2 2 27751
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 1.7 2 99.9 0.44 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 4FPZ 1.7 65.09 26350 1395 99.99 0.16346 0.16106 0.1734 0.21017 0.2185 RANDOM 25.713
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] -0.69 -0.35 -0.69 2.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.589 r_dihedral_angle_4_deg 21.393 r_dihedral_angle_3_deg 12.59 r_long_range_B_other 6.797 r_long_range_B_refined 6.795 r_dihedral_angle_1_deg 5.866 r_scangle_other 5.069 r_scbond_it 3.469 r_scbond_other 3.436 r_mcangle_it 3.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.589 r_dihedral_angle_4_deg 21.393 r_dihedral_angle_3_deg 12.59 r_long_range_B_other 6.797 r_long_range_B_refined 6.795 r_dihedral_angle_1_deg 5.866 r_scangle_other 5.069 r_scbond_it 3.469 r_scbond_other 3.436 r_mcangle_it 3.119 r_mcangle_other 3.118 r_mcbond_it 2.409 r_mcbond_other 2.4 r_angle_refined_deg 2.013 r_angle_other_deg 1.101 r_chiral_restr 0.116 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 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 258 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing