1UXS

CRYSTAL STRUCTURE OF HLA-B*2705 COMPLEXED WITH THE LATENT MEMBRANE PROTEIN 2 PEPTIDE (LMP2)OF EPSTEIN-BARR VIRUS


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1K5NPDB ENTRY 1K5N

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.1M TRIS, PH 7.5, 15% PEG8000
Crystal Properties
Matthews coefficientSolvent content
2.956.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.136α = 90
b = 82.329β = 109.25
c = 65.91γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2003-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.2BESSY14.2

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
11.5562990.051213.3744382
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)
11.551.61970.24642.6

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1K5N1.5562.0270657375599.20.1430.1420.177RANDOM17.61
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]
-1.940.080.81.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.875
r_scangle_it6.233
r_mcangle_it4.882
r_scbond_it4.657
r_mcbond_it3.953
r_angle_refined_deg1.47
r_angle_other_deg0.847
r_symmetry_vdw_other0.323
r_nbd_other0.255
r_nbd_refined0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.875
r_scangle_it6.233
r_mcangle_it4.882
r_scbond_it4.657
r_mcbond_it3.953
r_angle_refined_deg1.47
r_angle_other_deg0.847
r_symmetry_vdw_other0.323
r_nbd_other0.255
r_nbd_refined0.2
r_symmetry_hbond_refined0.16
r_xyhbond_nbd_refined0.143
r_symmetry_vdw_refined0.103
r_chiral_restr0.098
r_nbtor_other0.082
r_bond_refined_d0.015
r_gen_planes_other0.01
r_gen_planes_refined0.009
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3181
Nucleic Acid Atoms
Solvent Atoms710
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing