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Crystal structure of 10-mer peptide from EBV in complex with HLA-A1101.
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 4.6 290 0.2 M ammonium acetate, 0.1 M Sodium acetate trihydrate, 30% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.44 49.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.422 α = 90 b = 67.795 β = 90 c = 115.295 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 2015-09-25 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 1.8 58.44 96.7 6.85 3 37049
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 1.8 58.44 37049 1912 96.63 0.17928 0.17686 0.1882 0.22595 0.2347 RANDOM 23.484
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] -0.24 -0.05 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.596 r_dihedral_angle_4_deg 18.756 r_dihedral_angle_3_deg 13.854 r_dihedral_angle_1_deg 6.758 r_long_range_B_refined 6.758 r_long_range_B_other 6.757 r_scangle_other 4.731 r_mcangle_it 3.138 r_mcangle_other 3.137 r_scbond_it 3.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.596 r_dihedral_angle_4_deg 18.756 r_dihedral_angle_3_deg 13.854 r_dihedral_angle_1_deg 6.758 r_long_range_B_refined 6.758 r_long_range_B_other 6.757 r_scangle_other 4.731 r_mcangle_it 3.138 r_mcangle_other 3.137 r_scbond_it 3.128 r_scbond_other 3.128 r_mcbond_it 2.206 r_mcbond_other 2.204 r_angle_refined_deg 1.881 r_angle_other_deg 1.046 r_chiral_restr 0.117 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 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 3132 Nucleic Acid Atoms Solvent Atoms 413 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing