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ASLTVS segment from Human Immunoglobulin Light-Chain Variable Domain, Residues 73-78, assembled as an amyloid fibril
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other IDEAL beta strand
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 0.1 M Malic Acid, MES:Tris buffer, 25% PEG 1500
Crystal Properties Matthews coefficient Solvent content 1.42 13.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 15.167 α = 90 b = 11.58 β = 97.32 c = 18.798 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 ADSC QUANTUM 315 2012-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9792 APS 24-ID-E
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 1.3 100 80.5 0.192 5.6 2.5 1351
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 1.3 1.4 62.5 0.27 1.5
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 IDEAL beta strand 1.3 18.64 1215 130 79.59 0.1861 0.1826 0.1902 0.218 0.2205 RANDOM 6.422
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] 1.8 0.12 -0.61 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 9.165 r_dihedral_angle_1_deg 7.466 r_angle_refined_deg 2.085 r_angle_other_deg 0.954 r_chiral_restr 0.132 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 80 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction