6TDO

Crystal structure of the disulfide engineered HLA-A0201 molecule in complex with one GM dipeptide in the A pocket.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6Q3K 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2980.2 M magnesium acetate, 0.1 M sodium cacodylate pH 6.5, and 20% PEG 800
Crystal Properties
Matthews coefficientSolvent content
2.5351.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.936α = 90
b = 80.914β = 112.74
c = 56.351γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.987EMBL/DESY, HAMBURGX13

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.658199.90.0560.9911.36.952645
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.690.780.49

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 REPLACEMENTTHROUGHOUT6Q3K1.6551.9749987260799.850.18760.18570.2237RANDOM19.664
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]
0.12-0.22-0.210.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.228
r_dihedral_angle_4_deg18.086
r_dihedral_angle_3_deg13.377
r_dihedral_angle_1_deg6.906
r_angle_refined_deg1.833
r_angle_other_deg1.081
r_chiral_restr0.096
r_bond_refined_d0.015
r_gen_planes_refined0.012
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.228
r_dihedral_angle_4_deg18.086
r_dihedral_angle_3_deg13.377
r_dihedral_angle_1_deg6.906
r_angle_refined_deg1.833
r_angle_other_deg1.081
r_chiral_restr0.096
r_bond_refined_d0.015
r_gen_planes_refined0.012
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3077
Nucleic Acid Atoms
Solvent Atoms522
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing