5M00

Crystal structure of murine P14 TCR complex with H-2Db and Y4A, modified gp33 peptide from LCMV


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829319% PEG 6000, 0.1M Tris HCl pH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.7555

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 258.455α = 90
b = 46.941β = 94.24
c = 90.253γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-09-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.972ESRFID23-1

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
11.95128.997.90.04313.1377777
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)
11.951.99960.5483.14274

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 REPLACEMENTTHROUGHOUT1s7u1.95128.8773882389497.580.201480.199580.23715RANDOM42.426
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]
-0.12-0.340.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.367
r_dihedral_angle_4_deg17.101
r_dihedral_angle_3_deg15.253
r_dihedral_angle_1_deg7.11
r_long_range_B_refined6.17
r_long_range_B_other6.169
r_scangle_other2.165
r_mcangle_it1.826
r_mcangle_other1.826
r_angle_refined_deg1.667
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.367
r_dihedral_angle_4_deg17.101
r_dihedral_angle_3_deg15.253
r_dihedral_angle_1_deg7.11
r_long_range_B_refined6.17
r_long_range_B_other6.169
r_scangle_other2.165
r_mcangle_it1.826
r_mcangle_other1.826
r_angle_refined_deg1.667
r_scbond_it1.338
r_scbond_other1.338
r_mcbond_it1.112
r_mcbond_other1.112
r_angle_other_deg0.988
r_chiral_restr0.099
r_bond_refined_d0.014
r_gen_planes_refined0.008
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 Atoms6504
Nucleic Acid Atoms
Solvent Atoms381
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing