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Structure of full-length human lambda-6A light chain JTO in complex with stabilizer 34 [3-(2-(7-(diethylamino)-4-methyl-2-oxo-2H-chromen-3-yl)ethyl)-7-(1H-imidazole-5-carbonyl)-1,3,7-triazaspiro[4.4]nonane-2,4-dione]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MG5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 296 20% PEG 3350 and 0.25 M NH4H2PO4 at 23 degrees C
Crystal Properties Matthews coefficient Solvent content 2.72 54.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.884 α = 90 b = 82.846 β = 90 c = 95.382 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 100 PIXEL DECTRIS EIGER X 16M 2019-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
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 1.99 47.74 99.8 0.117 0.035 1 13.3 12.3 35344 22
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 1.99 2.1 98.7 1.008 0.298 0.85 2.5 12.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6MG5 1.99 47.74 33544 1742 99.78 0.1784 0.176 0.1904 0.2248 0.233 RANDOM 35.738
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] -2.34 5.07 -2.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.51 r_dihedral_angle_4_deg 16.149 r_dihedral_angle_3_deg 14.421 r_dihedral_angle_1_deg 7.838 r_angle_other_deg 2.417 r_angle_refined_deg 1.544 r_chiral_restr 0.066 r_bond_other_d 0.036 r_gen_planes_other 0.01 r_bond_refined_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.51 r_dihedral_angle_4_deg 16.149 r_dihedral_angle_3_deg 14.421 r_dihedral_angle_1_deg 7.838 r_angle_other_deg 2.417 r_angle_refined_deg 1.544 r_chiral_restr 0.066 r_bond_other_d 0.036 r_gen_planes_other 0.01 r_bond_refined_d 0.009 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3260 Nucleic Acid Atoms Solvent Atoms 385 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling PHASER phasing