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Crystal structure of HLA-B*2709 complexed with the vasoactive intestinal peptide type 1 receptor (VIPR) peptide (residues 400-408)
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 VAPOR DIFFUSION, HANGING DROP 8.5 291 TRIS PH 8.5, 19% PEG 8000 HANGING DROP, TEMPERATURE 291K
Crystal Properties Matthews coefficient Solvent content 2.9 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.158 α = 90 b = 81.635 β = 107.47 c = 65.31 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 MARRESEARCH 2002-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
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 2.2 29.1 96 0.12 9.7 3.1 25005
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 2.2 2.28 97 0.35 4.1 3
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 2.2 62.02 23736 1267 95.8 0.191 0.188 0.1862 0.244 0.235 RANDOM 33.81
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 1.17 0.01 0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.788 r_scangle_it 2.842 r_scbond_it 1.711 r_angle_refined_deg 1.259 r_mcangle_it 1.117 r_angle_other_deg 0.815 r_mcbond_it 0.611 r_symmetry_vdw_other 0.295 r_nbd_other 0.245 r_nbd_refined 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.788 r_scangle_it 2.842 r_scbond_it 1.711 r_angle_refined_deg 1.259 r_mcangle_it 1.117 r_angle_other_deg 0.815 r_mcbond_it 0.611 r_symmetry_vdw_other 0.295 r_nbd_other 0.245 r_nbd_refined 0.18 r_xyhbond_nbd_refined 0.178 r_symmetry_hbond_refined 0.167 r_symmetry_vdw_refined 0.109 r_chiral_restr 0.081 r_nbtor_other 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined 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 r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3191 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing