6MJJ

Crystal structure of the mCD1d/xxm (JJ290) /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
3.1260.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.999α = 90
b = 191.279β = 90
c = 151.264γ = 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
11.935099.90.0940.1020.0395.26.686000
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)
11.931.9699.90.7050.7680.3030.8326.3

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 REPLACEMENTTHROUGHOUT4IRS1.9347.8781727422999.710.18590.18430.2164RANDOM30.716
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]
-0.151.07-0.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.492
r_dihedral_angle_4_deg13.985
r_dihedral_angle_3_deg11.938
r_dihedral_angle_1_deg6.542
r_angle_refined_deg0.919
r_angle_other_deg0.75
r_chiral_restr0.044
r_bond_refined_d0.004
r_gen_planes_refined0.003
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.492
r_dihedral_angle_4_deg13.985
r_dihedral_angle_3_deg11.938
r_dihedral_angle_1_deg6.542
r_angle_refined_deg0.919
r_angle_other_deg0.75
r_chiral_restr0.044
r_bond_refined_d0.004
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 Atoms6347
Nucleic Acid Atoms
Solvent Atoms702
Heterogen Atoms218

Software

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