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The high resolution crystal structure of HLA-B*1402 complexed with a Cathepsin A signal sequence peptide, pCatA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BVN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 24- 27%(w/v) PEG 20000, with 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.56 52.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.791 α = 90 b = 82.144 β = 90 c = 110.734 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 2007-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 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 1.864 50 96.8 0.07 20.14 4.6 38358 38358
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 1.864 1.93 0.24 3.6 3022
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3BVN 1.864 50 2 38358 36391 1918 97.15 0.17181 0.16931 0.21904 0.2043 RANDOM 20.459
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] 0.45 -0.92 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.422 r_dihedral_angle_4_deg 19.748 r_dihedral_angle_3_deg 14.144 r_dihedral_angle_1_deg 5.93 r_scangle_it 3.997 r_scbond_it 2.508 r_mcangle_it 1.558 r_angle_refined_deg 1.441 r_mcbond_it 0.975 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.422 r_dihedral_angle_4_deg 19.748 r_dihedral_angle_3_deg 14.144 r_dihedral_angle_1_deg 5.93 r_scangle_it 3.997 r_scbond_it 2.508 r_mcangle_it 1.558 r_angle_refined_deg 1.441 r_mcbond_it 0.975 r_nbtor_refined 0.303 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.198 r_xyhbond_nbd_refined 0.163 r_symmetry_hbond_refined 0.153 r_chiral_restr 0.113 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3153 Nucleic Acid Atoms Solvent Atoms 551 Heterogen Atoms 24
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling