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Structure of the germline Vk1 O18/O8 light chain variable domain homodimer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BRE polyserine model of pdb entry 1BRE chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 Protein: 890 micromolar in 10 mM TRIS pH 7.4. Mother Liquor: 15-30% (w/v) PEG 4K, 0.2 Li2SO4, 0.1 M TRIS pH 7.9-8.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.29 62.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.265 α = 90 b = 74.265 β = 90 c = 99.051 γ = 120
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 1.3 99 99.7 0.046 53.2 12.2 74839 74839 22.2
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) 1.3 1.33 96.3 0.53 2.3 5.6 5311
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT polyserine model of pdb entry 1BRE chain A 1.3 99 74839 74839 535 99.19 0.11955 0.11935 0.14815 0.1642 RANDOM 14.491
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] 0.06 0.03 0.06 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.932 r_dihedral_angle_4_deg 19.808 r_sphericity_free 16.821 r_dihedral_angle_3_deg 11.163 r_dihedral_angle_1_deg 6.402 r_scangle_it 5.511 r_scbond_it 4.5 r_sphericity_bonded 4.388 r_mcangle_it 2.977 r_mcbond_it 2.459
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.932 r_dihedral_angle_4_deg 19.808 r_sphericity_free 16.821 r_dihedral_angle_3_deg 11.163 r_dihedral_angle_1_deg 6.402 r_scangle_it 5.511 r_scbond_it 4.5 r_sphericity_bonded 4.388 r_mcangle_it 2.977 r_mcbond_it 2.459 r_rigid_bond_restr 2.333 r_angle_other_deg 2.164 r_angle_refined_deg 1.773 r_mcbond_other 1.682 r_xyhbond_nbd_refined 0.301 r_nbd_refined 0.265 r_symmetry_vdw_other 0.232 r_nbd_other 0.225 r_symmetry_hbond_refined 0.224 r_nbtor_refined 0.193 r_symmetry_vdw_refined 0.132 r_chiral_restr 0.117 r_nbtor_other 0.091 r_xyhbond_nbd_other 0.062 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_gen_planes_other 0.007 r_bond_other_d 0.003 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1970 Nucleic Acid Atoms Solvent Atoms 454 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling PHASER phasing