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CRYSTAL STRUCTURE OF CATHEPSIN D ZYMOGEN FROM THE TICK IXODES RICINUS (IRCD1)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 1:1 PROTEIN (10 MG/ML IN 2 MM BIS- TRIS, PH 6.5, 20 MM SODIUM CHLORIDE) TO RESERVOIR (0.085 M TRIS-HCL, PH 8.0, 1.7 M AMMONIUM SULFATE, 1 MM DTT), CRYOCOOLED IN MOTHER LIQUOR, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
Crystal Properties Matthews coefficient Solvent content 2.95 58.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.322 α = 90 b = 94.981 β = 99.28 c = 106.17 γ = 90
Symmetry Space Group P 1 21 1
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 315r 2013-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 1.07161 ESRF ID14-1
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 2.3 45.87 99.7 0.069 14.81 4.1 82782 -3
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 2.3 2.44 99.3 0.479 2.79
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 2.3 45.87 78636 4145 99.73 0.22218 0.22017 0.2215 0.25999 0.2635 RANDOM 40.185
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] -0.16 -0.04 0.13 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.824 r_dihedral_angle_4_deg 19.141 r_dihedral_angle_3_deg 15.359 r_dihedral_angle_1_deg 7.288 r_long_range_B_refined 5.45 r_long_range_B_other 5.45 r_scangle_other 3.609 r_mcangle_it 3.386 r_mcangle_other 3.386 r_scbond_it 2.235
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.824 r_dihedral_angle_4_deg 19.141 r_dihedral_angle_3_deg 15.359 r_dihedral_angle_1_deg 7.288 r_long_range_B_refined 5.45 r_long_range_B_other 5.45 r_scangle_other 3.609 r_mcangle_it 3.386 r_mcangle_other 3.386 r_scbond_it 2.235 r_scbond_other 2.227 r_mcbond_it 2.096 r_mcbond_other 2.096 r_angle_refined_deg 1.45 r_angle_other_deg 0.97 r_chiral_restr 0.087 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 10963 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling