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Structure of HLA-A2:01 with peptide G11N
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 2.7 54.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.268 α = 90 b = 79.509 β = 115.96 c = 58.281 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 315 2015-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.12 SSRL BL7-1
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 2.3 50 96.6 0.071 21.2 3.4 19954
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 2.3 2.38 81.9 0.335 3.3 3.1
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 2.3 50 18963 975 96.36 0.21172 0.20936 0.2129 0.25733 0.2571 RANDOM 47.692
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] 0.04 0.03 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.262 r_dihedral_angle_4_deg 15.709 r_dihedral_angle_3_deg 14.315 r_dihedral_angle_1_deg 6.613 r_long_range_B_refined 5.377 r_long_range_B_other 5.376 r_scangle_other 3.585 r_mcangle_it 3.053 r_mcangle_other 3.052 r_scbond_it 2.147
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.262 r_dihedral_angle_4_deg 15.709 r_dihedral_angle_3_deg 14.315 r_dihedral_angle_1_deg 6.613 r_long_range_B_refined 5.377 r_long_range_B_other 5.376 r_scangle_other 3.585 r_mcangle_it 3.053 r_mcangle_other 3.052 r_scbond_it 2.147 r_scbond_other 2.147 r_mcbond_other 1.916 r_mcbond_it 1.915 r_angle_refined_deg 1.22 r_angle_other_deg 0.869 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 3079 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing Coot model building