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GNNQQNY peptide corresponding to residues 7-13 of yeast prion sup35
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 EVAPORATION, RECRYSTALLIZATION 298 peptide was dissolved at 10 mg/mL in water, quickly filtered, and left to sit at room temperature, EVAPORATION, RECRYSTALLIZATION, temperature 298K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 23.324 α = 90 b = 4.934 β = 90 c = 37.548 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 2005-07-16 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 2 19.81 96.4 0.248 4.61 380 -3 2.446
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) 2 2.2 98.9 0.417 2.7 90
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 2 19.81 372 18 94.66 0.242 0.241 0.2446 0.252 0.2392 RANDOM 12.533
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] 0.05 0.19 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 56.115 r_dihedral_angle_3_deg 11.183 r_dihedral_angle_1_deg 7.418 r_mcangle_it 3.309 r_mcbond_it 2.691 r_scangle_it 2.561 r_scbond_it 2.295 r_angle_refined_deg 1.544 r_mcbond_other 0.873 r_angle_other_deg 0.635
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 56.115 r_dihedral_angle_3_deg 11.183 r_dihedral_angle_1_deg 7.418 r_mcangle_it 3.309 r_mcbond_it 2.691 r_scangle_it 2.561 r_scbond_it 2.295 r_angle_refined_deg 1.544 r_mcbond_other 0.873 r_angle_other_deg 0.635 r_nbd_other 0.18 r_nbtor_refined 0.18 r_symmetry_vdw_other 0.159 r_symmetry_vdw_refined 0.153 r_xyhbond_nbd_refined 0.149 r_nbd_refined 0.123 r_chiral_restr 0.104 r_nbtor_other 0.085 r_symmetry_hbond_refined 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 59 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction