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A Native to Amyloidogenic Transition Regulated by a Backbone Trigger
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LDS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 295 31% PEG 4000, 25% glycerol, 0.2M ammonium acetate, 0.1M sodium acetate; drops contained 1ul of ~19 mg/ml protein, 1ul of mother liquor, and 1ul of 0.05M sodium acetate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.34 47.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.948 α = 90 b = 89.948 β = 90 c = 54.76 γ = 90
Symmetry Space Group P 43 21 2
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 2005-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 0.97660 NSLS X25
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 1.7 50 99.8 0.059 6 25244 25232 -3
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 1.7 1.76 99.6 0.827 5.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1LDS 1.7 46.78 25241 23868 1288 99.66 0.18587 0.1838 0.1944 0.22717 0.238 RANDOM 29.657
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] 0.26 0.26 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.47 r_dihedral_angle_4_deg 13.733 r_dihedral_angle_3_deg 8.821 r_scangle_it 5.206 r_dihedral_angle_1_deg 4.39 r_scbond_it 4.252 r_mcbond_it 4.12 r_mcangle_it 3.778 r_angle_refined_deg 1.091 r_mcbond_other 0.766
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.47 r_dihedral_angle_4_deg 13.733 r_dihedral_angle_3_deg 8.821 r_scangle_it 5.206 r_dihedral_angle_1_deg 4.39 r_scbond_it 4.252 r_mcbond_it 4.12 r_mcangle_it 3.778 r_angle_refined_deg 1.091 r_mcbond_other 0.766 r_angle_other_deg 0.674 r_symmetry_vdw_other 0.219 r_nbd_other 0.197 r_nbd_refined 0.184 r_nbtor_refined 0.176 r_symmetry_hbond_refined 0.166 r_xyhbond_nbd_refined 0.163 r_symmetry_vdw_refined 0.127 r_nbtor_other 0.079 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_bond_other_d 0.007 r_gen_planes_refined 0.004 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1564 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction CBASS data collection