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Structure of HLA-A2:01 with peptide MM91
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ENW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295.15 30% PEG 4000, 0.1M TRIS-HCL PH 8.5,
0.2M LITHIUM SULFATE
Crystal Properties Matthews coefficient Solvent content 2.53 51.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.99 α = 90 b = 80.861 β = 113.32 c = 56.933 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 PILATUS3 S 6M 2018-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.979 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.58 40 96.5 0.054 0.064 0.033 9.4 3.4 58659
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.58 1.62 88.4 0.35 0.429 0.242 0.835 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 5ENW 1.58 32 56646 1710 96.66 0.18 0.1793 0.1898 0.2049 0.2114 RANDOM 18.843
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] -0.01 0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.335 r_dihedral_angle_4_deg 16.349 r_dihedral_angle_3_deg 12.383 r_dihedral_angle_1_deg 6.611 r_angle_other_deg 1.33 r_angle_refined_deg 1.299 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.335 r_dihedral_angle_4_deg 16.349 r_dihedral_angle_3_deg 12.383 r_dihedral_angle_1_deg 6.611 r_angle_other_deg 1.33 r_angle_refined_deg 1.299 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3099 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms 22
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing