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The high resolution crystal structure of HLA-B*2705 in complex with a Cathepsin A signal sequence peptide pCatA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BP7 PDB ENTRY 3BP7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 23% PEG 8000, 0.1M Tris buffer pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.58 52.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.161 α = 90 b = 82.4 β = 90 c = 109.846 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 MARRESEARCH Mirrors 2006-01-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.95373 BESSY 14.2
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 1.85 50 95.8 0.08 12.41 3.1 38830
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 83.7 0.311 0.311 3.08 2.7 3323
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 3BP7 1.85 46.63 38786 1929 95.83 0.175 0.173 0.1815 0.222 0.2238 RANDOM 20.192
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 35.221 r_dihedral_angle_4_deg 15.494 r_dihedral_angle_3_deg 13.27 r_dihedral_angle_1_deg 6.711 r_scangle_it 4.385 r_scbond_it 3.144 r_mcangle_it 1.942 r_angle_refined_deg 1.823 r_mcbond_it 1.725 r_angle_other_deg 0.931
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.221 r_dihedral_angle_4_deg 15.494 r_dihedral_angle_3_deg 13.27 r_dihedral_angle_1_deg 6.711 r_scangle_it 4.385 r_scbond_it 3.144 r_mcangle_it 1.942 r_angle_refined_deg 1.823 r_mcbond_it 1.725 r_angle_other_deg 0.931 r_mcbond_other 0.38 r_symmetry_vdw_other 0.359 r_symmetry_hbond_refined 0.243 r_nbd_refined 0.213 r_nbd_other 0.206 r_xyhbond_nbd_refined 0.198 r_symmetry_vdw_refined 0.186 r_chiral_restr 0.116 r_nbtor_other 0.09 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3159 Nucleic Acid Atoms Solvent Atoms 502 Heterogen Atoms 12
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling