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Altered dimer interface decreases stability in an amyloidogenic kappa1 Bence Jones protein.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Vk1 O18/O8 germline variable light chain domain monomer
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 295 Mother Liquor: 15-30% (w/v) PEG 4K, 0.2 M Li2SO4, 0.1 M TRIS pH 7.9-8.9. Protein: 890 micromolar in 10 mM TRIS, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 4.75 74.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 176.054 α = 90 b = 176.054 β = 90 c = 176.054 γ = 90
Symmetry Space Group P 41 3 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 SBC-3 mirror 2007-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 1.0718 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.55 176 99.3 0.095 82.5 98.7 29819 29819 50.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.55 2.64 93 0.47 9.8 68.3 2094
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 Vk1 O18/O8 germline variable light chain domain monomer 2.55 35.21 29819 29819 529 97.73 0.1662 0.16547 0.232 0.20601 0.253 RANDOM 18.458
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 r_dihedral_angle_2_deg 42.93 r_dihedral_angle_3_deg 17.465 r_dihedral_angle_4_deg 12.731 r_dihedral_angle_1_deg 8.026 r_scangle_it 3.316 r_scbond_it 2.145 r_angle_refined_deg 1.832 r_angle_other_deg 1.292 r_mcangle_it 1.161 r_mcbond_it 0.829
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.93 r_dihedral_angle_3_deg 17.465 r_dihedral_angle_4_deg 12.731 r_dihedral_angle_1_deg 8.026 r_scangle_it 3.316 r_scbond_it 2.145 r_angle_refined_deg 1.832 r_angle_other_deg 1.292 r_mcangle_it 1.161 r_mcbond_it 0.829 r_symmetry_vdw_refined 0.344 r_symmetry_vdw_other 0.235 r_nbd_other 0.217 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.2 r_nbtor_refined 0.188 r_symmetry_hbond_refined 0.178 r_mcbond_other 0.172 r_chiral_restr 0.097 r_nbtor_other 0.095 r_xyhbond_nbd_other 0.055 r_bond_refined_d 0.02 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 3490 Nucleic Acid Atoms Solvent Atoms 443 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling PHASER phasing