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Crystal structure of HLA A2*01-AVYDGREHTV
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5E00
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M potassium sodium tartrate, 0.1 M bis-tris propane pH6.5, 20 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.67 53.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.97 α = 90 b = 80.69 β = 115.13 c = 58.66 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 PIXEL DECTRIS PILATUS 6M-F 2017-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9282 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 48.31 99.5 0.055 0.028 12.2 3.6 102850 15.236
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.37 99.7 1.139 0.659 1 2.9
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 FREE R-VALUE 5e00 1.35 48.31 97575 5245 99.47 0.1627 0.1607 0.1697 0.2003 0.2077 RANDOM 23.166
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] -1.27 0.32 2.38 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.402 r_dihedral_angle_4_deg 19.286 r_dihedral_angle_3_deg 11.317 r_dihedral_angle_1_deg 6.491 r_rigid_bond_restr 5.642 r_angle_refined_deg 1.467 r_angle_other_deg 1.317 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.402 r_dihedral_angle_4_deg 19.286 r_dihedral_angle_3_deg 11.317 r_dihedral_angle_1_deg 6.491 r_rigid_bond_restr 5.642 r_angle_refined_deg 1.467 r_angle_other_deg 1.317 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3139 Nucleic Acid Atoms Solvent Atoms 439 Heterogen Atoms 12
Software Software Software Name Purpose xia2 data scaling REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction PHASER phasing