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NFVFGT segment from Human Immunoglobulin Light-Chain Variable Domain, Residues 98-103, assembled as an amyloid fibril
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.1 M Imidazole, 20% PEG 3000, 0.2 M Zinc Acetate
Crystal Properties Matthews coefficient Solvent content 1.46 15.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 16.03 α = 90.89 b = 11.66 β = 103.23 c = 21.94 γ = 90.26
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 DECTRIS PILATUS 6M-F 2015-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9717 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 21.35 81.8 0.066 0.077 0.997 12.83 3.424 6835 8.571
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1 1.07 60.4 0.124 0.148 0.982 6.73 3.177
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 AB INITIO PHASING THROUGHOUT NO Starting model, We used DIRECT METHODS 1 21.35 6154 684 81.83 0.1048 0.1025 0.1013 0.1247 0.1231 RANDOM 7.488
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] -0.38 -0.24 -0.18 -0.03 -0.02 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.969 r_rigid_bond_restr 20.279 r_sphericity_free 17.741 r_dihedral_angle_3_deg 12.47 r_dihedral_angle_1_deg 8.046 r_sphericity_bonded 6.447 r_angle_refined_deg 1.589 r_angle_other_deg 1.477 r_chiral_restr 0.086 r_gen_planes_other 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.969 r_rigid_bond_restr 20.279 r_sphericity_free 17.741 r_dihedral_angle_3_deg 12.47 r_dihedral_angle_1_deg 8.046 r_sphericity_bonded 6.447 r_angle_refined_deg 1.589 r_angle_other_deg 1.477 r_chiral_restr 0.086 r_gen_planes_other 0.01 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 196 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction SHELXD phasing