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Structure of an early native-like intermediate of beta2-microglobulin amyloidosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X89 pdb entry 2X89
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M MES, 1.6 M MgSO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.66 66.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.79 α = 90 b = 96.79 β = 90 c = 167.79 γ = 90
Symmetry Space Group P 42 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 PIXEL DECTRIS PILATUS 6M 2012-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97950 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 50 99.9 14.3 25281 25281
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.67 99.8 1.01 14.7
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 pdb entry 2X89 2.6 48.43 25281 24016 1264 99.89 0.22847 0.22607 0.2286 0.2737 0.2719 RANDOM 58.836
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] -0.84 -0.84 1.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.611 r_dihedral_angle_4_deg 19.742 r_dihedral_angle_3_deg 17.179 r_dihedral_angle_1_deg 7.371 r_angle_other_deg 3.657 r_mcangle_it 2.767 r_scbond_it 2.383 r_mcbond_it 1.622 r_mcbond_other 1.622 r_angle_refined_deg 1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.611 r_dihedral_angle_4_deg 19.742 r_dihedral_angle_3_deg 17.179 r_dihedral_angle_1_deg 7.371 r_angle_other_deg 3.657 r_mcangle_it 2.767 r_scbond_it 2.383 r_mcbond_it 1.622 r_mcbond_other 1.622 r_angle_refined_deg 1.55 r_chiral_restr 0.086 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_gen_planes_other 0.009 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3564 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 42
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XDS data scaling