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Crystal structure of the complex of Ribosome inactivating protein from Momordica Balsamina with peptidoglycan fragment at 1.78 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 6.8 298 14% PEG 6000, 0.1M Sodium Phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.42 49.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.239 α = 90 b = 130.239 β = 90 c = 40.113 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 1.78 50 99.8 0.046 30.2 23001 23001
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 1.78 1.81 96.5 0.429 2
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 1.78 32.58 23001 1235 99.68 0.1839 0.18243 0.1892 0.20122 0.2158 RANDOM 29.711
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] -0.85 -0.85 -0.85 2.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.65 r_dihedral_angle_4_deg 18.822 r_dihedral_angle_3_deg 12.775 r_long_range_B_refined 5.635 r_long_range_B_other 5.285 r_dihedral_angle_1_deg 5.043 r_scangle_other 1.88 r_mcangle_it 1.64 r_mcangle_other 1.639 r_angle_refined_deg 1.174
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.65 r_dihedral_angle_4_deg 18.822 r_dihedral_angle_3_deg 12.775 r_long_range_B_refined 5.635 r_long_range_B_other 5.285 r_dihedral_angle_1_deg 5.043 r_scangle_other 1.88 r_mcangle_it 1.64 r_mcangle_other 1.639 r_angle_refined_deg 1.174 r_scbond_it 1.097 r_scbond_other 1.097 r_mcbond_it 0.949 r_mcbond_other 0.948 r_angle_other_deg 0.819 r_chiral_restr 0.061 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_gen_planes_other 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1911 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 59
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling