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Structure of the complex of type 1 ribosome inactivating protein from Momordica balsamina with a nucleotide, cytidine monophosphate at 1.80 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S9Q
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 2.4 48.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.98 α = 90 b = 129.98 β = 90 c = 40.066 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 77 CCD MARRESEARCH 2012-11-11 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 1.8 37.77 100 0.049 62.7 4.3 22210 22210
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 1.8 1.83 99.6 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 3S9Q 1.8 37.77 22210 1205 99.3 0.18426 0.18293 0.1849 0.20872 0.208 RANDOM 32.267
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] -1.33 -1.33 -1.33 4.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.021 r_dihedral_angle_4_deg 12.355 r_dihedral_angle_3_deg 11.781 r_long_range_B_refined 5.232 r_long_range_B_other 5.232 r_dihedral_angle_1_deg 4.935 r_scangle_other 1.847 r_mcangle_it 1.475 r_mcangle_other 1.475 r_scbond_it 1.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.021 r_dihedral_angle_4_deg 12.355 r_dihedral_angle_3_deg 11.781 r_long_range_B_refined 5.232 r_long_range_B_other 5.232 r_dihedral_angle_1_deg 4.935 r_scangle_other 1.847 r_mcangle_it 1.475 r_mcangle_other 1.475 r_scbond_it 1.114 r_scbond_other 1.105 r_angle_refined_deg 1.051 r_mcbond_it 0.878 r_mcbond_other 0.877 r_angle_other_deg 0.715 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 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 1911 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling Coot model building