8D5Q

TCR TG6 in complex with Ld-HF10


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LD91LD9, 3TO4
experimental modelPDB 3TO41LD9, 3TO4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP27711 % w/v PEG 8000, 0.1 M MES 6.0, 0.24 M Ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.9257.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.963α = 90
b = 89.963β = 90
c = 105.982γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.9792APS24-ID-E

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.59099.80.0326.66.429168
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.540.29

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTNONE1LD9, 3TO42.50145.02229168149399.8390.1720.16880.22265.211
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]
-0.251-0.2510.501
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.114
r_dihedral_angle_4_deg21.23
r_dihedral_angle_3_deg19.361
r_lrange_it10.022
r_lrange_other10.021
r_dihedral_angle_1_deg8.557
r_scangle_it7.36
r_scangle_other7.359
r_mcangle_it6.184
r_mcangle_other6.183
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.114
r_dihedral_angle_4_deg21.23
r_dihedral_angle_3_deg19.361
r_lrange_it10.022
r_lrange_other10.021
r_dihedral_angle_1_deg8.557
r_scangle_it7.36
r_scangle_other7.359
r_mcangle_it6.184
r_mcangle_other6.183
r_scbond_it4.996
r_scbond_other4.854
r_mcbond_it4.167
r_mcbond_other4.166
r_angle_refined_deg1.892
r_angle_other_deg1.372
r_symmetry_nbd_refined0.262
r_symmetry_xyhbond_nbd_refined0.235
r_nbd_refined0.21
r_symmetry_nbd_other0.205
r_nbd_other0.192
r_nbtor_refined0.181
r_xyhbond_nbd_refined0.168
r_symmetry_nbtor_other0.088
r_chiral_restr0.087
r_symmetry_xyhbond_nbd_other0.063
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5108
Nucleic Acid Atoms
Solvent Atoms208
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing