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Structure of NNQQ Peptide from Yeast Prion SUP35
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other polyalanine ideal beta-strand
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 15.479 α = 90 b = 4.915 β = 90 c = 30.552 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 MAR CCD 165 mm 2005-12-19 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 1.4 90 74.9 0.124 8.7 3.1 426 426 -3 18.8
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) 1.4 1.45 54.3 0.209 2.8 25
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 (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 polyalanine ideal beta-strand 1.42 15.28 426 413 39 74.28 0.188 0.183 0.1916 0.235 0.2271 RANDOM 8.984
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] -1.11 -0.85 1.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.192 r_dihedral_angle_3_deg 10.806 r_scbond_it 9.714 r_scangle_it 7.745 r_mcangle_it 6.638 r_sphericity_bonded 6.513 r_mcbond_it 6.472 r_rigid_bond_restr 6.143 r_dihedral_angle_1_deg 4.135 r_mcbond_other 3.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.192 r_dihedral_angle_3_deg 10.806 r_scbond_it 9.714 r_scangle_it 7.745 r_mcangle_it 6.638 r_sphericity_bonded 6.513 r_mcbond_it 6.472 r_rigid_bond_restr 6.143 r_dihedral_angle_1_deg 4.135 r_mcbond_other 3.013 r_angle_refined_deg 1.397 r_angle_other_deg 0.615 r_nbd_other 0.18 r_chiral_restr 0.166 r_symmetry_vdw_other 0.137 r_nbtor_refined 0.133 r_symmetry_hbond_refined 0.108 r_nbtor_other 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 35 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction