6MG4

Structure of full-length human lambda-6A light chain JTO


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. Crystals were harvested and immediately flash cooled in liquid nitrogen.
Crystal Properties
Matthews coefficientSolvent content
2.7154.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.385α = 90
b = 82.464β = 90
c = 97.017γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS PILATUS3 6M2018-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.0332APS23-ID-D

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
11.7544.6697.50.0550.0340.9618.23.55081428
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)
11.751.7886.20.490.290.842.13.4

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 REPLACEMENTTHROUGHOUT1LIL1.7544.6648204256097.290.1730.1710.221RANDOM37
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]
-1.824.41-2.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.151
r_dihedral_angle_4_deg15.595
r_dihedral_angle_3_deg12.31
r_long_range_B_refined9.424
r_long_range_B_other9.203
r_dihedral_angle_1_deg7.173
r_scangle_other6.443
r_mcangle_it4.248
r_mcangle_other4.247
r_scbond_it4.182
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.151
r_dihedral_angle_4_deg15.595
r_dihedral_angle_3_deg12.31
r_long_range_B_refined9.424
r_long_range_B_other9.203
r_dihedral_angle_1_deg7.173
r_scangle_other6.443
r_mcangle_it4.248
r_mcangle_other4.247
r_scbond_it4.182
r_scbond_other4.181
r_mcbond_it3.034
r_mcbond_other3.034
r_angle_refined_deg1.491
r_angle_other_deg0.543
r_chiral_restr0.074
r_bond_refined_d0.012
r_gen_planes_refined0.009
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 Atoms664
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing