7LMO

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]


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29620% PEG 3350 and 0.25 M NH4H2PO4 at 23 degrees C
Crystal Properties
Matthews coefficientSolvent content
2.7254.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.884α = 90
b = 82.846β = 90
c = 95.382γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.0332APS23-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.9947.7499.80.1170.035113.312.33534422
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)RedundancyNumber Unique Reflections (All)
11.992.198.71.0080.2980.852.512.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6MG51.9947.7433544174299.780.17840.1760.2248RANDOM35.738
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]
-2.345.07-2.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.51
r_dihedral_angle_4_deg16.149
r_dihedral_angle_3_deg14.421
r_dihedral_angle_1_deg7.838
r_angle_other_deg2.417
r_angle_refined_deg1.544
r_chiral_restr0.066
r_bond_other_d0.036
r_gen_planes_other0.01
r_bond_refined_d0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.51
r_dihedral_angle_4_deg16.149
r_dihedral_angle_3_deg14.421
r_dihedral_angle_1_deg7.838
r_angle_other_deg2.417
r_angle_refined_deg1.544
r_chiral_restr0.066
r_bond_other_d0.036
r_gen_planes_other0.01
r_bond_refined_d0.009
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3260
Nucleic Acid Atoms
Solvent Atoms385
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing