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Structure of full-length human lambda-6A light chain JTO in complex with stabilizer 62 [4-methyl-3-(morpholinomethyl)-7-(1-phenylethoxy)-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 54.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.133 α = 90 b = 81.09 β = 90 c = 96.301 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 CCD ADSC QUANTUM 315r 2019-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.976484 ALS 5.0.3
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 1.91 44.63 99.1 0.096 0.037 1 12.6 7.7 39458 17
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 1.91 2.01 1.033 0.278 0.95 2.3
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 1.91 44.63 37376 2020 99.11 0.1627 0.1605 0.1718 0.2027 0.2121 RANDOM 24.175
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] -0.45 0.28 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.084 r_dihedral_angle_4_deg 19.504 r_dihedral_angle_3_deg 13.789 r_dihedral_angle_1_deg 7.638 r_angle_other_deg 2.458 r_angle_refined_deg 1.724 r_chiral_restr 0.081 r_bond_other_d 0.036 r_gen_planes_other 0.013 r_bond_refined_d 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.084 r_dihedral_angle_4_deg 19.504 r_dihedral_angle_3_deg 13.789 r_dihedral_angle_1_deg 7.638 r_angle_other_deg 2.458 r_angle_refined_deg 1.724 r_chiral_restr 0.081 r_bond_other_d 0.036 r_gen_planes_other 0.013 r_bond_refined_d 0.012 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3257 Nucleic Acid Atoms Solvent Atoms 511 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling PHASER phasing