5FKP

Crystal structure of the mouse CD1d in complex with the p99 peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3G08PDB ENTRY 3G08

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.2M AMMONIUM TARTRATE AND 20% PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.6753.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.17α = 90
b = 107.57β = 90
c = 110.61γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-1SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.85599.50.0911.16.1472722
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.999.60.832.46.1

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 3G081.849.1944833237499.240.206810.205380.23361RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.408
r_dihedral_angle_4_deg16.478
r_dihedral_angle_3_deg11.77
r_long_range_B_other6.044
r_long_range_B_refined6.042
r_dihedral_angle_1_deg5.871
r_angle_refined_deg1.267
r_mcangle_it0.928
r_mcangle_other0.927
r_scangle_other0.905
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.408
r_dihedral_angle_4_deg16.478
r_dihedral_angle_3_deg11.77
r_long_range_B_other6.044
r_long_range_B_refined6.042
r_dihedral_angle_1_deg5.871
r_angle_refined_deg1.267
r_mcangle_it0.928
r_mcangle_other0.927
r_scangle_other0.905
r_angle_other_deg0.899
r_scbond_it0.566
r_scbond_other0.553
r_mcbond_it0.528
r_mcbond_other0.528
r_chiral_restr0.074
r_bond_refined_d0.007
r_gen_planes_refined0.005
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 Atoms3007
Nucleic Acid Atoms
Solvent Atoms272
Heterogen Atoms154

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing