6MG5

Structure of full-length human lambda-6A light chain JTO in complex with coumarin 1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP296Crystals of JTO-FL were grown via sitting-drop vapor diffusion using a crystallization buffer consisting of 20% PEG 3350 and 0.2 M NH4H2PO4 at 23 degrees C. Both diamond-shaped and plate-shaped crystals were generated in the same drop using these conditions, but only the plate-shaped crystals produced usable diffraction data. To generate JTO-FL:ligand complexes, crystals of apo JTO-FL were soaked with a tenfold molar excess of ligand for 10 days. Crystals were harvested and immediately flash cooled in liquid nitrogen.
Crystal Properties
Matthews coefficientSolvent content
2.7755.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.07α = 90
b = 84.219β = 90
c = 96.171γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS EIGER X 16M2018-04-06MSINGLE 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
11.845.1980.110.05119.55.24784225
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)
11.81.8595.91.590.760.4615

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.845.0944684231296.040.2070.2040.263RANDOM35
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]
-0.823.03-2.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.347
r_dihedral_angle_4_deg16.219
r_dihedral_angle_3_deg13.662
r_long_range_B_refined7.75
r_long_range_B_other7.749
r_dihedral_angle_1_deg7.342
r_scangle_other5.163
r_mcangle_it4.464
r_mcangle_other4.464
r_scbond_it3.443
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.347
r_dihedral_angle_4_deg16.219
r_dihedral_angle_3_deg13.662
r_long_range_B_refined7.75
r_long_range_B_other7.749
r_dihedral_angle_1_deg7.342
r_scangle_other5.163
r_mcangle_it4.464
r_mcangle_other4.464
r_scbond_it3.443
r_scbond_other3.442
r_mcbond_it2.874
r_mcbond_other2.874
r_angle_refined_deg1.401
r_angle_other_deg0.519
r_chiral_restr0.061
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3257
Nucleic Acid Atoms
Solvent Atoms493
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing