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Structure of HLA-A2:01 with peptide Y10L
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MRE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 30% PEG 4000, 0.1M Tris-HCl pH 8.0, 0.2M lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.65 53.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.384 α = 90 b = 79.492 β = 116.09 c = 57.208 γ = 90
Symmetry Space Group P 1 21 1
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 2015-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 12.3.1 0.73, 2.5 ALS 12.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.7 50 93.3 0.19 7.89 2.8 32562 11732
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 95.4 0.66 2.1 2.8
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 3MRE 2.7 48.18 11305 604 94.46 0.21662 0.21293 0.2157 0.28505 0.2832 RANDOM 19.796
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] -0.03 0.05 -0.06 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.167 r_dihedral_angle_4_deg 17.636 r_dihedral_angle_3_deg 16.867 r_dihedral_angle_1_deg 7.215 r_long_range_B_refined 3.126 r_long_range_B_other 3.126 r_mcangle_it 1.753 r_mcangle_other 1.753 r_scangle_other 1.626 r_angle_refined_deg 1.457
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.167 r_dihedral_angle_4_deg 17.636 r_dihedral_angle_3_deg 16.867 r_dihedral_angle_1_deg 7.215 r_long_range_B_refined 3.126 r_long_range_B_other 3.126 r_mcangle_it 1.753 r_mcangle_other 1.753 r_scangle_other 1.626 r_angle_refined_deg 1.457 r_mcbond_it 1.013 r_mcbond_other 1.012 r_angle_other_deg 0.961 r_scbond_it 0.945 r_scbond_other 0.945 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 3063 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing Coot model building