6CXA

Structure of alpha-GSA[20,6P] 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 DROP429520% PEG 3350, 8% Tacsimate pH 4.0
Crystal Properties
Matthews coefficientSolvent content
3.0159.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.051α = 90
b = 190.45β = 90
c = 151.085γ = 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
12.654097.20.120.1390.06973.532558
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)
12.652.7496.30.4930.5830.3020.3973.4

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 REPLACEMENTTHROUGHOUT3QUZ2.654030929160597.090.19790.1950.2532RANDOM52.62
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]
-1.014.38-3.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.814
r_dihedral_angle_4_deg15.289
r_dihedral_angle_3_deg14.966
r_dihedral_angle_1_deg6.69
r_angle_refined_deg1.322
r_angle_other_deg1.039
r_chiral_restr0.074
r_bond_refined_d0.009
r_bond_other_d0.004
r_gen_planes_refined0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.814
r_dihedral_angle_4_deg15.289
r_dihedral_angle_3_deg14.966
r_dihedral_angle_1_deg6.69
r_angle_refined_deg1.322
r_angle_other_deg1.039
r_chiral_restr0.074
r_bond_refined_d0.009
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 Atoms6362
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms150

Software

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