6C6C

Structure of glycolipid aGSA[20,6P] in complex with mouse CD1d


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Q7Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP429520% PEG 3350, 8% Tacsimate
Crystal Properties
Matthews coefficientSolvent content
2.4549.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.525α = 90
b = 98.339β = 106.25
c = 55.31γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-04-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.976SSRLBL9-2

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
12.085094.60.0590.0690.03563.524118
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)
12.082.1472.50.250.3060.1740.9352.5

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 REPLACEMENTTHROUGHOUT2Q7Y2.0836.12316992994.020.20130.19980.2409RANDOM39.609
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]
-0.010.010.02-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.454
r_dihedral_angle_4_deg15.341
r_dihedral_angle_3_deg14.613
r_dihedral_angle_1_deg6.173
r_angle_refined_deg1.426
r_angle_other_deg1.313
r_chiral_restr0.077
r_bond_refined_d0.009
r_bond_other_d0.007
r_gen_planes_refined0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.454
r_dihedral_angle_4_deg15.341
r_dihedral_angle_3_deg14.613
r_dihedral_angle_1_deg6.173
r_angle_refined_deg1.426
r_angle_other_deg1.313
r_chiral_restr0.077
r_bond_refined_d0.009
r_bond_other_d0.007
r_gen_planes_refined0.005
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2945
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms159

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction