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Structure of full-length human lambda-6A light chain JTO in complex with stabilizer 63 [4-methyl-3-(morpholinomethyl)-7-(2-phenylpropoxy)-2H-chromen-2-one]
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 2.7 54.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.742 α = 90 b = 81.938 β = 90 c = 95.826 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 2019-11-26 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 2.09 47.96 99.7 0.085 0.034 1 12.3 7.2 30392 30
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 2.09 2.2 98.1 0.649 0.251 1 2.9 7.6
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 6MG5 2.09 47.96 28513 1546 98.71 0.2046 0.2016 0.2606 0.2788 RANDOM 45.552
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] -2.96 6.69 -3.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.466 r_dihedral_angle_3_deg 13.7 r_dihedral_angle_4_deg 10.048 r_dihedral_angle_1_deg 7.932 r_angle_other_deg 2.439 r_angle_refined_deg 1.584 r_chiral_restr 0.064 r_bond_other_d 0.036 r_bond_refined_d 0.009 r_gen_planes_other 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.466 r_dihedral_angle_3_deg 13.7 r_dihedral_angle_4_deg 10.048 r_dihedral_angle_1_deg 7.932 r_angle_other_deg 2.439 r_angle_refined_deg 1.584 r_chiral_restr 0.064 r_bond_other_d 0.036 r_bond_refined_d 0.009 r_gen_planes_other 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3257 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling PHASER phasing