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Structure of amyloidogenic kappa 1 Bence Jones protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q20 pdb entry 2Q20
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 Protein: 923 mM in 10 mM Tris-HCl buffer, pH 7.4. Mother Liquor: 20% w/v polyethylene glycol 4000, 0.2 M Li2SO4, 0.1 M Tris buffer, pH 6.8, under 60% paraffin oil and 40% silicon oil, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.15 60.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.428 α = 90 b = 81.428 β = 90 c = 77.259 γ = 120
Symmetry Space Group P 61 2 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 IMAGE PLATE RIGAKU RAXIS IV++ Osmic VariMax 2007-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5241
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 1.8 77.15 93.8 0.036 17.2 3.66 14547 13965
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) 1.8 1.85 87.9 3.44 3.3 3.85 994
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 (All) 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 2Q20 1.8 77.15 14547 13965 594 99.54 0.19569 0.19569 0.19296 0.1909 0.26566 0.2626 RANDOM 39.491
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] 0.09 0.05 0.09 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.554 r_dihedral_angle_4_deg 24.057 r_dihedral_angle_3_deg 16.379 r_scangle_it 7.31 r_dihedral_angle_1_deg 7.087 r_scbond_it 5.648 r_mcangle_it 4.052 r_mcbond_it 2.791 r_angle_refined_deg 1.967 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.554 r_dihedral_angle_4_deg 24.057 r_dihedral_angle_3_deg 16.379 r_scangle_it 7.31 r_dihedral_angle_1_deg 7.087 r_scbond_it 5.648 r_mcangle_it 4.052 r_mcbond_it 2.791 r_angle_refined_deg 1.967 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.247 r_nbd_refined 0.232 r_symmetry_hbond_refined 0.214 r_xyhbond_nbd_refined 0.203 r_chiral_restr 0.135 r_bond_refined_d 0.026 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 905 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection CrystalClear data reduction CrystalClear data scaling PHASER phasing