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Structure of potato cathepsin D inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TC2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 2.0 M NaCl, 10% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.22 44.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.458 α = 90 b = 124.769 β = 95.14 c = 37.876 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS 2M 2015-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.917 Diamond I04-1
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 2.11 27.9 96 0.073 8.3 3.3 19943 19145
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 2.11 2.17 70.8 0.969 0.8 2.5
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 3TC2 2.12 64.38 18191 952 96.4 0.19544 0.19148 0.1989 0.26979 0.2699 RANDOM 48.877
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] 1.56 1.19 0.86 -2.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.177 r_dihedral_angle_4_deg 19.974 r_dihedral_angle_3_deg 16.85 r_long_range_B_refined 8.404 r_long_range_B_other 8.357 r_dihedral_angle_1_deg 7.643 r_scangle_other 5.601 r_mcangle_it 5.599 r_mcangle_other 5.597 r_mcbond_other 3.559
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.177 r_dihedral_angle_4_deg 19.974 r_dihedral_angle_3_deg 16.85 r_long_range_B_refined 8.404 r_long_range_B_other 8.357 r_dihedral_angle_1_deg 7.643 r_scangle_other 5.601 r_mcangle_it 5.599 r_mcangle_other 5.597 r_mcbond_other 3.559 r_mcbond_it 3.558 r_scbond_it 3.51 r_scbond_other 3.509 r_angle_refined_deg 1.629 r_angle_other_deg 0.997 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 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 2794 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing