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NNQQ peptide corresponding to residues 8-11 of yeast prion sup35 (alternate crystal form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YJP pdb entry 1yjp
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 30-50 mg/mL peptide disolved in water and mixed with an equal volume of reservoir solution consisting of 100 mM trisodium citrate, 20% polyethylene glycol 4000 and 20% isopropanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 4.854 α = 90 b = 16.014 β = 96.91 c = 15.546 γ = 90
Symmetry Space Group P 1 21 1
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 2005-07-16 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 90 63.8 0.152 10.1 1.5 259 20.4
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 26.1 0.299 1.2 23
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 pdb entry 1yjp 1.52 15.43 251 28 66.05 0.175 0.172 0.1869 0.202 0.2143 RANDOM 12.236
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] -1.65 0.39 0.16 1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 49.819 r_dihedral_angle_3_deg 12.152 r_mcangle_it 8.154 r_scangle_it 7.297 r_dihedral_angle_1_deg 6.443 r_scbond_it 5.002 r_mcbond_it 4.914 r_angle_refined_deg 1.314 r_mcbond_other 1.24 r_angle_other_deg 0.926
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 49.819 r_dihedral_angle_3_deg 12.152 r_mcangle_it 8.154 r_scangle_it 7.297 r_dihedral_angle_1_deg 6.443 r_scbond_it 5.002 r_mcbond_it 4.914 r_angle_refined_deg 1.314 r_mcbond_other 1.24 r_angle_other_deg 0.926 r_nbd_refined 0.201 r_symmetry_vdw_other 0.178 r_symmetry_hbond_refined 0.17 r_nbd_other 0.165 r_nbtor_refined 0.158 r_chiral_restr 0.148 r_nbtor_other 0.066 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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