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Structure of the amyloid-forming peptide Ac-LLQDIM-NH2 from human GHRH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other ideal beta strands
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION, RECRYSTALLIZATION 310 crystals formed on the wall of the tube during overnight incubation at 310 K from a 5 mg / ml solution at pH 4
Crystal Properties Matthews coefficient Solvent content 1.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.76 α = 90 b = 4.83 β = 112.008 c = 24.4 γ = 90
Symmetry Space Group C 1 2 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 PIXEL RIGAKU HyPix-6000HE 2024-02-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU PhotonJet-R 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 1.379 17.97 92.5 0.105 0.996 6.5 3.5 945 8.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.379 1.518 0.825 0.398
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.41 17.97 1.35 918 56 94.15 0.1393 0.1368 0.1373 0.1724 0.1702 8.89
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 21.8207 f_angle_d 1.3678 f_chiral_restr 0.0848 f_bond_d 0.0082 f_plane_restr 0.0041
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction XSCALE data scaling Fragon phasing