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Structure of Cathepsin D with inhibitor 2-bromo-N-[(2S,3S)-4-{[2-(2,4-dichlorophenyl)ethyl][3-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)propanoyl]amino}-3-hydroxy-1-(3-phenoxyphenyl)butan-2-yl]-4,5-dimethoxybenzamide
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 298 PEG 3350, pH 5.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.85 56.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.022 α = 90 b = 77.022 β = 90 c = 251.586 γ = 120
Symmetry Space Group P 61 2 2
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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.999 SLS X06SA
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 2.64 66.67 98.6 0.041 5.3 13822 2 93.29
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.64 2.78 99.9 0.85 0.94 1.99 5.4 1949
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 THROUGHOUT 2.64 45.76 13628 838 98.63 0.211 0.2068 0.2065 0.2818 0.2876 RANDOM 87.11
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] -2.0745 -2.0745 4.149
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.95 t_omega_torsion 3.25 t_angle_deg 1.22 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.95 t_omega_torsion 3.25 t_angle_deg 1.22 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2620 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 128
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling