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Crystal structure of HLA-B*2709 complexed with the glucagon receptor (GR) peptide (residues 412-420)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K5N PDB ENTRY 1K5N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 291 14% (w/v) PEG 4000, 20mM Tris/HCl pH 7.5, 150mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.85 56.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.946 α = 90 b = 81.933 β = 108.91 c = 65.397 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 2003-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.1 30 95.8 0.043 20.8 196702 -3 14.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.12 90.4 0.288 2.7
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 PDB ENTRY 1K5N 1.2 15 149186 3852 96.8 0.13 0.129 0.1409 0.149 0.1583 RANDOM 10.87
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] 0.12 -0.22 -0.15 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.892 r_dihedral_angle_4_deg 15.724 r_dihedral_angle_3_deg 11.31 r_sphericity_free 6.433 r_dihedral_angle_1_deg 6.098 r_sphericity_bonded 3.849 r_scangle_it 3.398 r_scbond_it 2.645 r_mcangle_it 1.983 r_mcbond_it 1.696
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.892 r_dihedral_angle_4_deg 15.724 r_dihedral_angle_3_deg 11.31 r_sphericity_free 6.433 r_dihedral_angle_1_deg 6.098 r_sphericity_bonded 3.849 r_scangle_it 3.398 r_scbond_it 2.645 r_mcangle_it 1.983 r_mcbond_it 1.696 r_rigid_bond_restr 1.453 r_angle_refined_deg 1.427 r_angle_other_deg 0.905 r_mcbond_other 0.631 r_symmetry_vdw_other 0.311 r_nbd_refined 0.214 r_nbd_other 0.209 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.145 r_symmetry_hbond_refined 0.143 r_symmetry_vdw_refined 0.096 r_chiral_restr 0.094 r_nbtor_other 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3192 Nucleic Acid Atoms Solvent Atoms 711 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling EPMR phasing