3O3D

Human Class I MHC HLA-A2 in complex with the Peptidomimetic ELA-2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5277PEG3350 24%, MES 0.025M, KCl 0.1M, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.346.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.16α = 90
b = 84.244β = 90.14
c = 84.123γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.98APS19-BM

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
11.72099.40.9114.93.689204886691117.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.71.7698.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2GT91.7208925588612443599.280.181640.181640.179680.21852RANDOM24.86
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]
-0.61.08-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.244
r_dihedral_angle_4_deg20.405
r_dihedral_angle_3_deg15.091
r_dihedral_angle_1_deg6.768
r_scangle_it4.556
r_scbond_it2.824
r_mcangle_it1.769
r_angle_refined_deg1.704
r_mcbond_it0.954
r_chiral_restr0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.244
r_dihedral_angle_4_deg20.405
r_dihedral_angle_3_deg15.091
r_dihedral_angle_1_deg6.768
r_scangle_it4.556
r_scbond_it2.824
r_mcangle_it1.769
r_angle_refined_deg1.704
r_mcbond_it0.954
r_chiral_restr0.14
r_bond_refined_d0.016
r_gen_planes_refined0.01
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_bond_other_d
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_sphericity_bonded
r_mcbond_other
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6312
Nucleic Acid Atoms
Solvent Atoms672
Heterogen Atoms30

Software

Software
Software NamePurpose
SBC-Collectdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling