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Crystal Structure of hla-b*2705 Complexed with the 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 7.5 281 0.1M Tris HCl, 24% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties Matthews coefficient Solvent content 2.56 51.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.661 α = 90 b = 82.797 β = 90 c = 110.286 γ = 90
Symmetry Space Group P 21 21 21
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) 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 95 0.093 13.3 41639
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 1.86 86.3 0.486 3713
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 1OGT 1.8 41.42 41581 2096 94.72 0.186 0.184 0.1902 0.223 0.2256 RANDOM 15.459
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.682 r_dihedral_angle_4_deg 15.826 r_dihedral_angle_3_deg 12.262 r_dihedral_angle_1_deg 5.605 r_scangle_it 2.082 r_scbond_it 1.305 r_angle_refined_deg 1.033 r_mcangle_it 0.88 r_mcbond_it 0.549 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.682 r_dihedral_angle_4_deg 15.826 r_dihedral_angle_3_deg 12.262 r_dihedral_angle_1_deg 5.605 r_scangle_it 2.082 r_scbond_it 1.305 r_angle_refined_deg 1.033 r_mcangle_it 0.88 r_mcbond_it 0.549 r_nbtor_refined 0.295 r_nbd_refined 0.183 r_xyhbond_nbd_refined 0.133 r_symmetry_vdw_refined 0.122 r_symmetry_hbond_refined 0.104 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3225 Nucleic Acid Atoms Solvent Atoms 555 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOLREP phasing