6JOZ

Crystal structure of BRLF peptide from EBV in complex with HLA-A1101.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X7Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52890.2M LITHIUM SULFATE MONOHYDRATE, 0.1M TRIS-HCL, 30% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.6854.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.395α = 90
b = 72.931β = 90
c = 125.699γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2017-03-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE TPS 05A1NSRRCTPS 05A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)CC (Half)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
11.3563.08970.080.9182.314.4101182
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.351.3850.5610.729

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 REPLACEMENTTHROUGHOUT1X7Q1.3563.0896217496996.90.161830.160440.1893RANDOM17.427
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]
0.16-0.190.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.833
r_dihedral_angle_4_deg17.107
r_dihedral_angle_3_deg11.895
r_long_range_B_refined6.921
r_long_range_B_other6.697
r_dihedral_angle_1_deg6.458
r_scangle_other5.528
r_scbond_it3.799
r_scbond_other3.771
r_mcangle_it2.538
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.833
r_dihedral_angle_4_deg17.107
r_dihedral_angle_3_deg11.895
r_long_range_B_refined6.921
r_long_range_B_other6.697
r_dihedral_angle_1_deg6.458
r_scangle_other5.528
r_scbond_it3.799
r_scbond_other3.771
r_mcangle_it2.538
r_mcangle_other2.538
r_angle_refined_deg2.492
r_mcbond_it1.805
r_mcbond_other1.805
r_angle_other_deg1.173
r_chiral_restr0.157
r_bond_refined_d0.03
r_gen_planes_refined0.013
r_bond_other_d0.003
r_gen_planes_other0.002
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 Atoms3131
Nucleic Acid Atoms
Solvent Atoms518
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing