6CX9

Structure of alpha-GSA[16,6P] bound by CD1d and in complex with the Va14Vb8.2 TCR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QUZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP429512% PEG 3350, 0.1M sodium malonate pH 4.0
Crystal Properties
Matthews coefficientSolvent content
359.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.891α = 90
b = 190.13β = 90
c = 151.043γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.98SSRLBL9-2

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
12.354092.60.0890.1010.0457.74.243262
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)
12.352.4393.70.4490.510.2310.7924.3

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 REPLACEMENTTHROUGHOUT3QUZ2.364041929133291.740.19350.19220.2351RANDOM47.189
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]
-0.290.84-0.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.528
r_dihedral_angle_4_deg14.387
r_dihedral_angle_3_deg13.729
r_dihedral_angle_1_deg6.34
r_angle_refined_deg1.275
r_angle_other_deg1.005
r_chiral_restr0.075
r_bond_refined_d0.008
r_bond_other_d0.004
r_gen_planes_refined0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.528
r_dihedral_angle_4_deg14.387
r_dihedral_angle_3_deg13.729
r_dihedral_angle_1_deg6.34
r_angle_refined_deg1.275
r_angle_other_deg1.005
r_chiral_restr0.075
r_bond_refined_d0.008
r_bond_other_d0.004
r_gen_planes_refined0.004
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6364
Nucleic Acid Atoms
Solvent Atoms203
Heterogen Atoms127

Software

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