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Crystal structure of HLA-B*2709 complexed with the double citrullinated 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 1OGT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 0.1M TRIS HCL,25% PEG 8000, , pH 8.000000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.93 58.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.176 α = 90 b = 82.428 β = 110.15 c = 67.017 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 2006-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.982 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 50 82.8 0.06 0.06 3.75 48072 39804 2
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) 1.8 1.84 91.9 0.432 2.49 3.76 2914
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1ogt 1.95 48.04 2 38149 32389 1614 84.9 0.227 0.201 0.199 0.1982 0.245 0.2448 RANDOM 19.765
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] -0.96 -0.43 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.315 r_dihedral_angle_4_deg 15.623 r_dihedral_angle_3_deg 14.63 r_dihedral_angle_1_deg 5.673 r_rigid_bond_restr 4.134 r_scbond_it 3.546 r_sphericity_free 3.389 r_scangle_it 3.052 r_sphericity_bonded 2.169 r_angle_refined_deg 1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.315 r_dihedral_angle_4_deg 15.623 r_dihedral_angle_3_deg 14.63 r_dihedral_angle_1_deg 5.673 r_rigid_bond_restr 4.134 r_scbond_it 3.546 r_sphericity_free 3.389 r_scangle_it 3.052 r_sphericity_bonded 2.169 r_angle_refined_deg 1.13 r_mcangle_it 1.08 r_mcbond_it 0.681 r_nbtor_refined 0.298 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.153 r_symmetry_vdw_refined 0.144 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3236 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction SCALEPACK data scaling PHASER phasing