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Crystal Structure of the Complex of type I Ribosome inactivating protein with hexapeptide Ser-Asp-Asp-Asp-Met-Gly at 2.2 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AHA PDB ENTRY 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 2.43 49.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.186 α = 90 b = 131.186 β = 90 c = 40.734 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 298 IMAGE PLATE MARRESEARCH Mirror 2009-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5414
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 2.22 65.7 99.2 0.056 12.6 12968 12968 42.124
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) 2.22 2.29 96.2 0.315 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1AHA 2.22 19.84 12968 12264 627 99.44 0.18626 0.18608 0.18292 0.1871 0.2219 0.245 RANDOM 42.229
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] -1.41 -0.7 -1.41 2.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.233 r_dihedral_angle_4_deg 25.32 r_dihedral_angle_3_deg 17.209 r_dihedral_angle_1_deg 5.367 r_scangle_it 3.37 r_scbond_it 2.148 r_angle_refined_deg 1.534 r_mcangle_it 1.351 r_mcbond_it 0.822 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.233 r_dihedral_angle_4_deg 25.32 r_dihedral_angle_3_deg 17.209 r_dihedral_angle_1_deg 5.367 r_scangle_it 3.37 r_scbond_it 2.148 r_angle_refined_deg 1.534 r_mcangle_it 1.351 r_mcbond_it 0.822 r_nbtor_refined 0.309 r_symmetry_hbond_refined 0.26 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.208 r_xyhbond_nbd_refined 0.19 r_chiral_restr 0.111 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1954 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 28
Software Software Software Name Purpose DENZO data reduction AMoRE phasing REFMAC refinement AUTOMAR data reduction SCALEPACK data scaling