7LMN

Structure of full-length human lambda-6A light chain JTO in complex with stabilizer 26 [2-(7-(diethylamino)-4-methyl-2-oxo-2H-chromen-3-yl)ethyl (3-(1H-imidazol-4-yl)benzyl)carbamate]


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6MG5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29620% PEG 3350 and 0.25 M NH4H2PO4 at 23 degrees C
Crystal Properties
Matthews coefficientSolvent content
2.7354.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.028α = 90
b = 82.131β = 90
c = 96.451γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2019-09-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.30.976484ALS5.0.3

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.0144.7899.60.0910.033114.17.83424028
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)
12.012.1297.20.720.2730.852.87.8

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 REPLACEMENTTHROUGHOUT6MG52.0144.7832449173399.540.190.18730.2393RANDOM37.217
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]
-1.743.81-2.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.794
r_dihedral_angle_4_deg19.482
r_dihedral_angle_3_deg14.643
r_dihedral_angle_1_deg7.517
r_angle_other_deg2.433
r_angle_refined_deg1.588
r_chiral_restr0.069
r_bond_other_d0.036
r_bond_refined_d0.009
r_gen_planes_other0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.794
r_dihedral_angle_4_deg19.482
r_dihedral_angle_3_deg14.643
r_dihedral_angle_1_deg7.517
r_angle_other_deg2.433
r_angle_refined_deg1.588
r_chiral_restr0.069
r_bond_other_d0.036
r_bond_refined_d0.009
r_gen_planes_other0.009
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3257
Nucleic Acid Atoms
Solvent Atoms342
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing