1UXW

CRYSTAL STRUCTURE OF HLA-B*2709 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
18.50.1M TRIS, PH 8.5, 21% PEG8000
Crystal Properties
Matthews coefficientSolvent content
2.956.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.92α = 90
b = 82.595β = 104.35
c = 62.79γ = 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
11.7260990.045203.3533532
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)
11.721.78960.26242.6

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 1K5N1.7160.8650633270398.90.1560.1540.19RANDOM13.13
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]
-0.59-0.120.080.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.118
r_scangle_it4.371
r_scbond_it2.695
r_mcangle_it1.715
r_angle_refined_deg1.586
r_mcbond_it0.965
r_angle_other_deg0.902
r_symmetry_vdw_other0.336
r_nbd_other0.26
r_nbd_refined0.204
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.118
r_scangle_it4.371
r_scbond_it2.695
r_mcangle_it1.715
r_angle_refined_deg1.586
r_mcbond_it0.965
r_angle_other_deg0.902
r_symmetry_vdw_other0.336
r_nbd_other0.26
r_nbd_refined0.204
r_xyhbond_nbd_refined0.147
r_symmetry_hbond_refined0.132
r_chiral_restr0.102
r_nbtor_other0.085
r_symmetry_vdw_refined0.079
r_bond_refined_d0.015
r_gen_planes_other0.012
r_gen_planes_refined0.01
r_bond_other_d0.003
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 Atoms3183
Nucleic Acid Atoms
Solvent Atoms596
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing