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Structure of SSTSSA, a fibril forming peptide from Bovine Pancreatic Ribonuclease (RNase A, residues 15-20)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other 5-residue beta strand SSTSA with the C-terminal alanine absent
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 Peptide concentration: 30 mg/ml, Reservoir: 0.1M HEPES-Na, pH 7.5, 10% v/v isopropanol, 20% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.008 α = 90 b = 4.83 β = 90 c = 12.888 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH 2005-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID13 ESRF ID13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.5 80 89.3 0.174 3.9 474 6.599
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.5 1.62 93.3 0.434 98
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 5 residue beta strand SSTSA with the C-terminal alanine absent 1.51 21 458 21 87.57 0.159 0.157 0.1551 0.219 0.2136 RANDOM 5.291
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 -0.02 0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 5.467 r_dihedral_angle_1_deg 5.242 r_angle_refined_deg 1.087 r_sphericity_bonded 0.714 r_angle_other_deg 0.693 r_mcangle_it 0.615 r_mcbond_it 0.488 r_rigid_bond_restr 0.409 r_sphericity_free 0.344 r_symmetry_vdw_other 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 5.467 r_dihedral_angle_1_deg 5.242 r_angle_refined_deg 1.087 r_sphericity_bonded 0.714 r_angle_other_deg 0.693 r_mcangle_it 0.615 r_mcbond_it 0.488 r_rigid_bond_restr 0.409 r_sphericity_free 0.344 r_symmetry_vdw_other 0.307 r_scbond_it 0.243 r_nbd_other 0.207 r_mcbond_other 0.164 r_scangle_it 0.137 r_nbtor_refined 0.122 r_nbtor_other 0.093 r_chiral_restr 0.064 r_symmetry_hbond_refined 0.06 r_symmetry_vdw_refined 0.053 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_refined 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 70 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction X-PLOR phasing