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Crystal structure of arginine inhibited Ribosome inactivating protein from Momordica balsamina at 1.69 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 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.41 48.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.315 α = 90 b = 130.315 β = 90 c = 39.952 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 1.69 50 99.8 0.059 57.5 26694 26694
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 1.7 1.73 99.9 0.586 2
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 (All) 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 SAD THROUGHOUT 3S9Q 1.69 32.6 26694 26694 1414 99.36 0.18845 0.18687 0.18542 0.1909 0.21369 0.2169 RANDOM 30.641
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] -1.05 -1.05 -1.05 3.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.258 r_dihedral_angle_4_deg 19.257 r_dihedral_angle_3_deg 13.16 r_long_range_B_refined 5.457 r_long_range_B_other 5.217 r_dihedral_angle_1_deg 5.024 r_scangle_other 2.21 r_mcangle_it 1.773 r_mcangle_other 1.773 r_scbond_it 1.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.258 r_dihedral_angle_4_deg 19.257 r_dihedral_angle_3_deg 13.16 r_long_range_B_refined 5.457 r_long_range_B_other 5.217 r_dihedral_angle_1_deg 5.024 r_scangle_other 2.21 r_mcangle_it 1.773 r_mcangle_other 1.773 r_scbond_it 1.304 r_scbond_other 1.303 r_angle_refined_deg 1.154 r_mcbond_it 1.032 r_mcbond_other 1.029 r_angle_other_deg 0.733 r_chiral_restr 0.062 r_bond_refined_d 0.005 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 234 Heterogen Atoms 38
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling