6CXF

Structure of alpha-GSA[26,P5p] 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 DROP4.129516% PEG 3350, 0.06M Citric acid, 0.04M BIS-TRIS propane pH 4.1
Crystal Properties
Matthews coefficientSolvent content
3.0459.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.933α = 90
b = 191.781β = 90
c = 151.378γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-11-20MSINGLE 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
12.55098.70.0890.1010.0466.44.439875
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)
12.52.5998.10.4720.5380.2520.8314

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 REPLACEMENTTHROUGHOUT3QUZ2.541.538053160198.680.19890.19710.2391RANDOM42.131
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]
0.022.1-2.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.424
r_dihedral_angle_3_deg13.866
r_dihedral_angle_4_deg13.539
r_dihedral_angle_1_deg6.518
r_angle_refined_deg1.321
r_angle_other_deg0.887
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.424
r_dihedral_angle_3_deg13.866
r_dihedral_angle_4_deg13.539
r_dihedral_angle_1_deg6.518
r_angle_refined_deg1.321
r_angle_other_deg0.887
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6338
Nucleic Acid Atoms
Solvent Atoms215
Heterogen Atoms157

Software

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