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Crystal structure of human cathepsin D in complex with macrocyclic inhibitor 9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QBH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291.15 25 % PEG 3350
0.2 lithium sulphate
0.1 Bis-Tris pH 5.5
Crystal Properties Matthews coefficient Solvent content 3.01 59.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.346 α = 90 b = 94.257 β = 90 c = 117.675 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS PILATUS 6M 2015-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 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 1.55 50 97.8 0.078 12.5 3.5 62404
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.6 88.5 0.953 0.622 1.02 2.8
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 6QBH 1.55 43.75 62404 2101 99.71 0.16713 0.16637 0.172 0.18977 0.1947 RANDOM 22.435
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] 0.65 0.39 -1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.007 r_dihedral_angle_4_deg 22.704 r_dihedral_angle_3_deg 12.548 r_dihedral_angle_1_deg 6.562 r_long_range_B_refined 5.181 r_long_range_B_other 5.181 r_scangle_other 3.769 r_scbond_it 2.564 r_scbond_other 2.563 r_mcangle_it 2.149
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.007 r_dihedral_angle_4_deg 22.704 r_dihedral_angle_3_deg 12.548 r_dihedral_angle_1_deg 6.562 r_long_range_B_refined 5.181 r_long_range_B_other 5.181 r_scangle_other 3.769 r_scbond_it 2.564 r_scbond_other 2.563 r_mcangle_it 2.149 r_mcangle_other 2.148 r_angle_refined_deg 1.74 r_mcbond_it 1.468 r_mcbond_other 1.467 r_angle_other_deg 1.072 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_gen_planes_other 0.005 r_bond_other_d 0.002 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 2592 Nucleic Acid Atoms Solvent Atoms 322 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing