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Crystal structure of dual peptide from EBV in complex with HLA-A*11:01
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X7Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 290 0.1 M Ammonium acetate, 0.1 M Bis-Tris, 22% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.43 49.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.246 α = 90 b = 67.432 β = 90 c = 115.017 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2015-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 0.9999 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.94 58.17 99.5 2.5 4.6 30594
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1X7Q 1.94 58.17 30594 1634 99.43 0.19177 0.18897 0.1967 0.24295 0.247 RANDOM 38.438
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] -1.95 0.76 1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.084 r_dihedral_angle_4_deg 21.666 r_dihedral_angle_3_deg 15.226 r_long_range_B_refined 7.709 r_long_range_B_other 7.708 r_dihedral_angle_1_deg 6.872 r_scangle_other 6.048 r_mcangle_it 4.647 r_mcangle_other 4.647 r_scbond_it 4.248
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.084 r_dihedral_angle_4_deg 21.666 r_dihedral_angle_3_deg 15.226 r_long_range_B_refined 7.709 r_long_range_B_other 7.708 r_dihedral_angle_1_deg 6.872 r_scangle_other 6.048 r_mcangle_it 4.647 r_mcangle_other 4.647 r_scbond_it 4.248 r_scbond_other 4.246 r_mcbond_it 3.402 r_mcbond_other 3.401 r_angle_refined_deg 1.777 r_angle_other_deg 1.032 r_chiral_restr 0.114 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 3125 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing