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Structure of full-length human lambda-6A light chain JTO
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LIL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 296 Crystals of JTO-FL were grown via sitting-drop vapor diffusion using a crystallization buffer consisting of 20% PEG 3350 and 0.2 M NH4H2PO4 at 23 degrees C. Both diamond-shaped and plate-shaped crystals were generated in the same drop using these conditions, but only the plate-shaped crystals produced usable diffraction data. Crystals were harvested and immediately flash cooled in liquid nitrogen.
Crystal Properties Matthews coefficient Solvent content 2.71 54.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.385 α = 90 b = 82.464 β = 90 c = 97.017 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS3 6M 2018-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rpim I (All) CC (Half) 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 1.75 44.66 97.5 0.055 0.034 0.96 18.2 3.5 50814 28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 86.2 0.49 0.29 0.84 2.1 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1LIL 1.75 44.66 48204 2560 97.29 0.173 0.171 0.221 0.25 RANDOM 37
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] -1.82 4.41 -2.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.151 r_dihedral_angle_4_deg 15.595 r_dihedral_angle_3_deg 12.31 r_long_range_B_refined 9.424 r_long_range_B_other 9.203 r_dihedral_angle_1_deg 7.173 r_scangle_other 6.443 r_mcangle_it 4.248 r_mcangle_other 4.247 r_scbond_it 4.182
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.151 r_dihedral_angle_4_deg 15.595 r_dihedral_angle_3_deg 12.31 r_long_range_B_refined 9.424 r_long_range_B_other 9.203 r_dihedral_angle_1_deg 7.173 r_scangle_other 6.443 r_mcangle_it 4.248 r_mcangle_other 4.247 r_scbond_it 4.182 r_scbond_other 4.181 r_mcbond_it 3.034 r_mcbond_other 3.034 r_angle_refined_deg 1.491 r_angle_other_deg 0.543 r_chiral_restr 0.074 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 3257 Nucleic Acid Atoms Solvent Atoms 664 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing