5D9S

Structure of HLA-A2:01 with the 11-mer peptide F11V


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.1530% PEG 5000 MME, 0.1M Tris-HCl pH 8.0, 0.2M lithium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.4950.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.33α = 90
b = 80.238β = 113.17
c = 56.855γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152015-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-11.12SSRLBL7-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.875099.825.63.536209
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.871.91992.73.3

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 REPLACEMENTTHROUGHOUT3MRE1.8726.5335062113099.590.190950.189890.22305RANDOM24.337
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]
-0.020.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.318
r_dihedral_angle_4_deg13.865
r_dihedral_angle_3_deg10.898
r_dihedral_angle_1_deg6.184
r_long_range_B_refined3.992
r_long_range_B_other3.991
r_scangle_other1.749
r_mcangle_it1.442
r_mcangle_other1.442
r_angle_refined_deg1.144
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.318
r_dihedral_angle_4_deg13.865
r_dihedral_angle_3_deg10.898
r_dihedral_angle_1_deg6.184
r_long_range_B_refined3.992
r_long_range_B_other3.991
r_scangle_other1.749
r_mcangle_it1.442
r_mcangle_other1.442
r_angle_refined_deg1.144
r_scbond_it1.035
r_scbond_other1.035
r_angle_other_deg0.86
r_mcbond_it0.847
r_mcbond_other0.847
r_chiral_restr0.072
r_bond_refined_d0.006
r_gen_planes_refined0.004
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 Atoms3105
Nucleic Acid Atoms
Solvent Atoms325
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
Cootmodel building
PHASERphasing