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CRYSTAL STRUCTURE OF MATURE CATHEPSIN D FROM THE TICK IXODES RICINUS (IRCD1) IN COMPLEX WITH THE N-TERMINAL OCTAPEPTIDE OF THE PROPEPTID
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 CRYSTALLIZATION CONDITIONS: 1:1 PROTEIN (5 MG/ML IN 5 MM TRIS-HCL,
REMARK 280 PH 7.0, 10% DMSO) TO RESERVOIR (0.2 M SODIUM ACETATE, 0.1 M SODIUM CACODYLATE, PH 6.5, 30% PEG8000), CRYOCOOLED AFTER A QUICK SOAK IN RESERVOIR BUFFER + 25% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
Crystal Properties Matthews coefficient Solvent content 2.18 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.925 α = 90 b = 63.925 β = 90 c = 80.496 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2013-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.979402 BESSY 14.1
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 45.2 99.4 0.052 16.18 6 30080
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 1.8 1.9 96.5 0.63 2.43 5.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FOURIER SYNTHESIS THROUGHOUT 1.81 45.2 28087 1479 99.37 0.18554 0.18312 0.1905 0.23094 0.235 RANDOM 39.517
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] 0.18 0.18 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.069 r_dihedral_angle_4_deg 15.969 r_dihedral_angle_3_deg 13.52 r_long_range_B_refined 7.364 r_long_range_B_other 7.364 r_dihedral_angle_1_deg 7.198 r_scangle_other 5.552 r_mcangle_it 4.533 r_mcangle_other 4.533 r_scbond_it 3.636
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.069 r_dihedral_angle_4_deg 15.969 r_dihedral_angle_3_deg 13.52 r_long_range_B_refined 7.364 r_long_range_B_other 7.364 r_dihedral_angle_1_deg 7.198 r_scangle_other 5.552 r_mcangle_it 4.533 r_mcangle_other 4.533 r_scbond_it 3.636 r_scbond_other 3.636 r_mcbond_it 3.163 r_mcbond_other 3.16 r_angle_refined_deg 1.658 r_angle_other_deg 1.01 r_chiral_restr 0.1 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2632 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling