☰ Navigation Tabs
Crystal structure of spermidine inhibited Ribosome inactivating protein from Momordica balsamina
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, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.41 48.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.152 α = 90 b = 130.152 β = 90 c = 40.059 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 mirror 2013-07-19 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 50 100 0.046 43.3 16729 16729
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 1.98 2.01 100 0.213 5.8
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 3S9Q 1.98 37.77 16729 16729 892 99.98 0.17011 0.16866 0.1751 0.19744 0.1983 RANDOM 31.73
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] -0.97 -0.97 -0.97 3.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.959 r_dihedral_angle_4_deg 19.159 r_dihedral_angle_3_deg 13.662 r_long_range_B_refined 5.244 r_long_range_B_other 5.244 r_dihedral_angle_1_deg 5.201 r_scangle_other 2.455 r_mcangle_it 2.028 r_mcangle_other 2.028 r_scbond_it 1.423
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.959 r_dihedral_angle_4_deg 19.159 r_dihedral_angle_3_deg 13.662 r_long_range_B_refined 5.244 r_long_range_B_other 5.244 r_dihedral_angle_1_deg 5.201 r_scangle_other 2.455 r_mcangle_it 2.028 r_mcangle_other 2.028 r_scbond_it 1.423 r_scbond_other 1.423 r_mcbond_it 1.181 r_mcbond_other 1.18 r_angle_refined_deg 1.154 r_angle_other_deg 0.745 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1911 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 36
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling