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The high resolution crystal structure of HLA-B*2709 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 1JGE PDB ENTRY 1JGE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 23.5% PEG 8000, 0.1M Tris buffer pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.63 53.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.195 α = 90 b = 83.002 β = 90 c = 110.779 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 2006-01-18 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 1.79 50 93.3 0.057 19.4 3.6 41600 19.9
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 1.79 1.85 84.3 0.331 3.07 3.3 3694
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 1JGE 1.8 46.08 41552 2090 92.85 0.169 0.167 0.1787 0.204 0.2147 RANDOM 14.028
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] 0.05 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.206 r_dihedral_angle_4_deg 16.717 r_dihedral_angle_3_deg 12.653 r_dihedral_angle_1_deg 6.356 r_scangle_it 3.887 r_scbond_it 2.815 r_angle_refined_deg 1.631 r_mcangle_it 1.628 r_mcbond_it 1.506 r_angle_other_deg 1.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.206 r_dihedral_angle_4_deg 16.717 r_dihedral_angle_3_deg 12.653 r_dihedral_angle_1_deg 6.356 r_scangle_it 3.887 r_scbond_it 2.815 r_angle_refined_deg 1.631 r_mcangle_it 1.628 r_mcbond_it 1.506 r_angle_other_deg 1.128 r_symmetry_vdw_other 0.306 r_mcbond_other 0.305 r_nbd_refined 0.215 r_nbd_other 0.204 r_xyhbond_nbd_refined 0.149 r_symmetry_hbond_refined 0.142 r_chiral_restr 0.107 r_symmetry_vdw_refined 0.104 r_nbtor_other 0.086 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3161 Nucleic Acid Atoms Solvent Atoms 513 Heterogen Atoms 6
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction