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Crystal structure of peptide 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 5 289 0.2M Sodium malonate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.07 60.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.502 α = 90 b = 90.525 β = 90 c = 91.24 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 1.66 64.27 99 0.07 0.951 2.4 7.2 64100
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 1.66 1.703 0.858 0.824
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 1.66 64.26 60966 3153 98.97 0.16702 0.16556 0.1768 0.19421 0.204 RANDOM 18.409
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] -0.14 0.23 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.083 r_dihedral_angle_4_deg 15.389 r_dihedral_angle_3_deg 14.322 r_long_range_B_other 7.893 r_long_range_B_refined 7.889 r_dihedral_angle_1_deg 6.372 r_scangle_other 5.747 r_scbond_it 3.765 r_scbond_other 3.741 r_mcangle_it 3.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.083 r_dihedral_angle_4_deg 15.389 r_dihedral_angle_3_deg 14.322 r_long_range_B_other 7.893 r_long_range_B_refined 7.889 r_dihedral_angle_1_deg 6.372 r_scangle_other 5.747 r_scbond_it 3.765 r_scbond_other 3.741 r_mcangle_it 3.091 r_mcangle_other 3.09 r_angle_refined_deg 2.296 r_mcbond_it 2.113 r_mcbond_other 2.113 r_angle_other_deg 1.159 r_chiral_restr 0.146 r_bond_refined_d 0.026 r_gen_planes_refined 0.013 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 3131 Nucleic Acid Atoms Solvent Atoms 447 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing