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Crystal structure of type 1 ribosome inactivating protein from Momordica balsamina in complex with guanosine mono phosphate at 1.75 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S9Q PDB ENTRY 3S9Q
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 2.4 48.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.072 α = 90 b = 130.072 β = 90 c = 39.877 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 MARMOSAIC 225 mm CCD Mirror 2014-04-07 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 1.75 65.04 100 0.039 41.75 4.8 25324 25324
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 99.7 0.554 2.4 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 3S9Q 1.75 65.04 25324 24033 1291 99.9 0.16702 0.16449 0.1742 0.21383 0.2162 RANDOM 34.461
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] -1.28 -0.64 -1.28 4.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.491 r_dihedral_angle_4_deg 21.287 r_dihedral_angle_3_deg 11.663 r_long_range_B_refined 8.085 r_long_range_B_other 8.085 r_scangle_other 5.894 r_dihedral_angle_1_deg 5.348 r_mcangle_it 4.026 r_mcangle_other 4.011 r_scbond_other 3.883
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.491 r_dihedral_angle_4_deg 21.287 r_dihedral_angle_3_deg 11.663 r_long_range_B_refined 8.085 r_long_range_B_other 8.085 r_scangle_other 5.894 r_dihedral_angle_1_deg 5.348 r_mcangle_it 4.026 r_mcangle_other 4.011 r_scbond_other 3.883 r_scbond_it 3.862 r_angle_other_deg 3.605 r_mcbond_it 2.819 r_mcbond_other 2.814 r_angle_refined_deg 1.834 r_chiral_restr 0.1 r_gen_planes_other 0.015 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 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 257 Heterogen Atoms 44
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling