6MJ6

Crystal structure of the mCD1d/xxx (JJ166) /iNKTCR ternary complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4IRS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2950.1 m sodium malonate pH 4.0, 12% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.0459.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.357α = 90
b = 191.02β = 90
c = 151.348γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.455097.90.0960.1050.0425.75.941815
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.452.5485.40.5190.5780.2480.8314.8

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 REPLACEMENTTHROUGHOUT4IRS2.4547.839659211497.850.19110.18870.2335RANDOM47.326
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]
-1.63.58-1.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.97
r_dihedral_angle_4_deg16.617
r_dihedral_angle_3_deg13.609
r_dihedral_angle_1_deg6.641
r_angle_refined_deg1.006
r_angle_other_deg0.73
r_chiral_restr0.045
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.97
r_dihedral_angle_4_deg16.617
r_dihedral_angle_3_deg13.609
r_dihedral_angle_1_deg6.641
r_angle_refined_deg1.006
r_angle_other_deg0.73
r_chiral_restr0.045
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6386
Nucleic Acid Atoms
Solvent Atoms267
Heterogen Atoms204

Software

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