6C6A

Structure of glycolipid aGSA[16,6P] 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 DROP729520% PEG 3350, 0.2M sodium malonate
Crystal Properties
Matthews coefficientSolvent content
2.754.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.171α = 90
b = 106.15β = 90
c = 107.037γ = 90
Symmetry
Space GroupP 21 21 21

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 BL9-20.98SSRLBL9-2

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
12.4550990.1140.1290.05944.518242
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)
12.452.5497.90.4590.5310.2590.8093.8

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 REPLACEMENTTHROUGHOUT2Q7Y2.45401725094898.820.21640.2140.2573RANDOM33.939
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]
-0.080.040.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.913
r_dihedral_angle_4_deg22.015
r_dihedral_angle_3_deg16.397
r_dihedral_angle_1_deg6.314
r_angle_refined_deg1.444
r_angle_other_deg1.205
r_chiral_restr0.076
r_bond_refined_d0.01
r_bond_other_d0.005
r_gen_planes_refined0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.913
r_dihedral_angle_4_deg22.015
r_dihedral_angle_3_deg16.397
r_dihedral_angle_1_deg6.314
r_angle_refined_deg1.444
r_angle_other_deg1.205
r_chiral_restr0.076
r_bond_refined_d0.01
r_bond_other_d0.005
r_gen_planes_refined0.005
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2980
Nucleic Acid Atoms
Solvent Atoms34
Heterogen Atoms110

Software

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