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Crystal structure of kappa 1 amyloidogenic light chain variable domain
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 5.4 295 Protein: 1.26 mM. Mother Liquor: 15% w/v polyethylene glycol 8000, 0.05 M magnesium acetate, 0.1 M sodium acetate, 0.1 M Tris buffer, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.39 48.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.02 α = 90 b = 47.02 β = 90 c = 103.356 γ = 90
Symmetry Space Group P 41 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 IMAGE PLATE RIGAKU RAXIS IV++ Osmic VariMax optics 2007-11-20 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 1.53 103.14 91 0.072 20.6 16.62 18394 16734
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) 1.53 1.58 35.7 0.365 4.3
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 (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 1.53 103.14 18394 16194 534 91.11 0.19138 0.19138 0.18949 0.2234 0.25144 0.284 RANDOM 18.622
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] -0.4 -0.4 0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.39 r_dihedral_angle_4_deg 17.859 r_dihedral_angle_3_deg 14.452 r_sphericity_free 9.015 r_dihedral_angle_1_deg 7.148 r_scangle_it 4.76 r_sphericity_bonded 4.064 r_scbond_it 3.605 r_mcangle_it 2.529 r_rigid_bond_restr 2.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.39 r_dihedral_angle_4_deg 17.859 r_dihedral_angle_3_deg 14.452 r_sphericity_free 9.015 r_dihedral_angle_1_deg 7.148 r_scangle_it 4.76 r_sphericity_bonded 4.064 r_scbond_it 3.605 r_mcangle_it 2.529 r_rigid_bond_restr 2.128 r_angle_refined_deg 1.88 r_mcbond_it 1.879 r_nbtor_refined 0.31 r_nbd_refined 0.218 r_symmetry_hbond_refined 0.199 r_symmetry_vdw_refined 0.196 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.146 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 916 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection CrystalClear data reduction CrystalClear data scaling PHASER phasing