☰ Navigation Tabs
Structure of full-length human lambda-6A light chain JTO in complex with stabilizer 36 [3-(2-(7-(diethylamino)-4-methyl-2-oxo-2H-chromen-3-yl)ethyl)-8-(1H-imidazole-4-carbonyl)-1,3,8-triazaspiro[4.5]decane-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 2.69 54.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.304 α = 90 b = 81.717 β = 90 c = 94.996 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 2.29 47.54 99.9 0.13 0.037 1 13.9 13.3 23063 25
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 2.29 2.42 99.1 1.008 0.298 0.82 2.3 13.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6MG5 2.29 47.54 21851 1158 99.81 0.2056 0.2025 0.2063 0.2639 0.2655 RANDOM 36.568
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] -1.2 1.1 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.314 r_dihedral_angle_4_deg 18.276 r_dihedral_angle_3_deg 15.47 r_dihedral_angle_1_deg 7.929 r_angle_other_deg 2.442 r_angle_refined_deg 1.559 r_chiral_restr 0.065 r_bond_other_d 0.036 r_bond_refined_d 0.008 r_gen_planes_other 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.314 r_dihedral_angle_4_deg 18.276 r_dihedral_angle_3_deg 15.47 r_dihedral_angle_1_deg 7.929 r_angle_other_deg 2.442 r_angle_refined_deg 1.559 r_chiral_restr 0.065 r_bond_other_d 0.036 r_bond_refined_d 0.008 r_gen_planes_other 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3260 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling PHASER phasing