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Crystal structure of BRLF 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 8.5 289 0.2M LITHIUM SULFATE MONOHYDRATE,
0.1M TRIS-HCL, 30% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.68 54.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.395 α = 90 b = 72.931 β = 90 c = 125.699 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 RAYONIX MX300-HS 2017-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 1.35 63.08 97 0.08 0.918 2.31 4.4 101182
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.385 0.561 0.729
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 1.35 63.08 96217 4969 96.9 0.16183 0.16044 0.1605 0.1893 0.189 RANDOM 17.427
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 -0.19 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.833 r_dihedral_angle_4_deg 17.107 r_dihedral_angle_3_deg 11.895 r_long_range_B_refined 6.921 r_long_range_B_other 6.697 r_dihedral_angle_1_deg 6.458 r_scangle_other 5.528 r_scbond_it 3.799 r_scbond_other 3.771 r_mcangle_it 2.538
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.833 r_dihedral_angle_4_deg 17.107 r_dihedral_angle_3_deg 11.895 r_long_range_B_refined 6.921 r_long_range_B_other 6.697 r_dihedral_angle_1_deg 6.458 r_scangle_other 5.528 r_scbond_it 3.799 r_scbond_other 3.771 r_mcangle_it 2.538 r_mcangle_other 2.538 r_angle_refined_deg 2.492 r_mcbond_it 1.805 r_mcbond_other 1.805 r_angle_other_deg 1.173 r_chiral_restr 0.157 r_bond_refined_d 0.03 r_gen_planes_refined 0.013 r_bond_other_d 0.003 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 3131 Nucleic Acid Atoms Solvent Atoms 518 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing