5EFI

Crystal structure of mouse CD1d in complex with the p99p lipopeptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3G08 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277ammonium citrate, PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.6753.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.19α = 90
b = 107.85β = 90
c = 110.34γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2014-01-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.9794SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.849.1297.410.93.546178

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 REPLACEMENTTHROUGHOUT3G081.849.1243789234596.890.219880.218570.24387RANDOM34.966
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]
-1.610.21.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.069
r_dihedral_angle_4_deg16.734
r_dihedral_angle_3_deg12.12
r_dihedral_angle_1_deg6.448
r_long_range_B_refined5.149
r_long_range_B_other5.149
r_angle_refined_deg1.334
r_angle_other_deg0.847
r_mcangle_it0.758
r_mcangle_other0.758
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.069
r_dihedral_angle_4_deg16.734
r_dihedral_angle_3_deg12.12
r_dihedral_angle_1_deg6.448
r_long_range_B_refined5.149
r_long_range_B_other5.149
r_angle_refined_deg1.334
r_angle_other_deg0.847
r_mcangle_it0.758
r_mcangle_other0.758
r_scangle_other0.639
r_mcbond_it0.426
r_mcbond_other0.426
r_scbond_it0.365
r_scbond_other0.364
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2980
Nucleic Acid Atoms
Solvent Atoms204
Heterogen Atoms154

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building