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The human non-classical major histocompatibility complex molecule HLA-E
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MHE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 293 14-19% PEG 3350, 2% MPD, 0.2M MgCl2, 0.1M Tris, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.62 52.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.778 α = 90 b = 73.354 β = 112.7 c = 131.535 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 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C APS 14-BM-C
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 2.5 50 0.052 21.6 63040
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 1MHE 2.5 15 59588 3180 98.6 0.2449 0.24216 0.2553 0.29625 0.2996 RANDOM 28.048
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] 2.66 0.35 0.69 -3.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.1 r_dihedral_angle_4_deg 23.241 r_dihedral_angle_3_deg 16.737 r_scangle_it 9.115 r_scbond_it 6.429 r_dihedral_angle_1_deg 4.784 r_mcangle_it 4.029 r_angle_refined_deg 2.904 r_mcbond_it 2.645 r_symmetry_hbond_refined 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.1 r_dihedral_angle_4_deg 23.241 r_dihedral_angle_3_deg 16.737 r_scangle_it 9.115 r_scbond_it 6.429 r_dihedral_angle_1_deg 4.784 r_mcangle_it 4.029 r_angle_refined_deg 2.904 r_mcbond_it 2.645 r_symmetry_hbond_refined 0.63 r_symmetry_vdw_refined 0.517 r_nbtor_refined 0.342 r_nbd_refined 0.338 r_xyhbond_nbd_refined 0.325 r_chiral_restr 0.103 r_bond_refined_d 0.025 r_gen_planes_refined 0.016 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12529 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement