5MEN

Human Leukocyte Antigen A02 presenting ILAKFLHWL, in complex with cognate T-Cell Receptor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4I4W 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2M ammonium sulphate, 0.1M HEPES pH7, 20% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.7154.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.16α = 90
b = 48.69β = 108.15
c = 118.1γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2011-05-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9778DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)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
12.80956.11299.70.10.1420.0729.23.72503125031
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)
12.812.8899.80.730.93.7

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 REPLACEMENTTHROUGHOUT4I4W2.8138.0323666126799.570.19310.18870.2724RANDOM57.144
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]
2.720.48-2.57-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.201
r_dihedral_angle_3_deg21.982
r_dihedral_angle_4_deg17.374
r_dihedral_angle_1_deg9.516
r_angle_refined_deg2.025
r_mcangle_it1.958
r_angle_other_deg1.191
r_mcbond_it1.139
r_mcbond_other1.139
r_chiral_restr0.129
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.201
r_dihedral_angle_3_deg21.982
r_dihedral_angle_4_deg17.374
r_dihedral_angle_1_deg9.516
r_angle_refined_deg2.025
r_mcangle_it1.958
r_angle_other_deg1.191
r_mcbond_it1.139
r_mcbond_other1.139
r_chiral_restr0.129
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6629
Nucleic Acid Atoms
Solvent Atoms59
Heterogen Atoms51

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction