☰ Navigation Tabs
Crystal Structure of the complex of type I ribosome inactivating protein from momordica balsamina with 5-(hydroxymethyl)oxalane-2,3,4-triol at 1.6 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AHA
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 49.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.972 α = 90 b = 129.972 β = 90 c = 40.245 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 2009-07-24 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 1.6 65 99 0.08 51.5 31379 31379 20.3
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 1.6 1.63 92.8 0.31 4.3
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 MOLECULAR REPLACEMENT THROUGHOUT 1AHA 1.6 64.99 31379 31379 1677 99.06 0.17109 0.17108 0.16978 0.1717 0.19542 0.1982 RANDOM 23.459
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] -0.74 -0.37 -0.74 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.21 r_dihedral_angle_4_deg 19.254 r_dihedral_angle_3_deg 12.22 r_dihedral_angle_1_deg 5.196 r_scangle_it 3.923 r_scbond_it 2.407 r_mcangle_it 1.406 r_angle_refined_deg 1.339 r_mcbond_it 0.739 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.21 r_dihedral_angle_4_deg 19.254 r_dihedral_angle_3_deg 12.22 r_dihedral_angle_1_deg 5.196 r_scangle_it 3.923 r_scbond_it 2.407 r_mcangle_it 1.406 r_angle_refined_deg 1.339 r_mcbond_it 0.739 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1911 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 36
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling