6OJP

Structure of glycolipid alpha-GSA[8,6P] in complex with mouse CD1d


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Q7YPDB entry 2Q7Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29520% PEG3350, 8% Tacsimate, pH 4.0
Crystal Properties
Matthews coefficientSolvent content
2.6753.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.891α = 90
b = 105.666β = 90
c = 106.672γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-05-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.976SSRLBL11-1

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
12.174089.90.0790.090.0419.54.123559
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)
12.172.2584.50.4360.510.2570.8253.2

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 REPLACEMENTTHROUGHOUTPDB entry 2Q7Y2.1736.6122156114990.120.21240.21060.2457RANDOM35.495
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]
-1.973.63-1.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.303
r_dihedral_angle_4_deg18.747
r_dihedral_angle_3_deg13.558
r_dihedral_angle_1_deg6.872
r_angle_refined_deg1.214
r_angle_other_deg1.073
r_chiral_restr0.041
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.303
r_dihedral_angle_4_deg18.747
r_dihedral_angle_3_deg13.558
r_dihedral_angle_1_deg6.872
r_angle_refined_deg1.214
r_angle_other_deg1.073
r_chiral_restr0.041
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2953
Nucleic Acid Atoms
Solvent Atoms84
Heterogen Atoms253

Software

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