☰ Navigation Tabs
The structure of cathepsin S with a novel 2-arylphenoxyacetaldehyde inhibitor derived by the Substrate Activity Screening (SAS) method
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F1G pdb entry 2F1G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1M NaAcetate, 20% Peg-8000 and 2.0M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.82 56.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.384 α = 90 b = 85.384 β = 90 c = 151.2 γ = 90
Symmetry Space Group P 41 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 CCD ADSC QUANTUM 315 2005-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 ALS 5.0.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.6 43.4 100 0.082 0.082 45.6 13.3 74679 74679
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) 1.6 1.66 100 0.725 0.725 5 13.2 7367
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT pdb entry 2F1G 1.6 43.4 70645 3738 100 0.15929 0.15929 0.15815 0.18063 RANDOM 13.335
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] 0.06 0.06 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.146 r_dihedral_angle_4_deg 13.293 r_dihedral_angle_3_deg 10.528 r_dihedral_angle_1_deg 5.536 r_scangle_it 3.625 r_scbond_it 2.464 r_mcangle_it 1.472 r_angle_refined_deg 1.367 r_mcbond_it 0.983 r_angle_other_deg 0.833
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.146 r_dihedral_angle_4_deg 13.293 r_dihedral_angle_3_deg 10.528 r_dihedral_angle_1_deg 5.536 r_scangle_it 3.625 r_scbond_it 2.464 r_mcangle_it 1.472 r_angle_refined_deg 1.367 r_mcbond_it 0.983 r_angle_other_deg 0.833 r_symmetry_vdw_refined 0.731 r_mcbond_other 0.231 r_nbd_refined 0.211 r_symmetry_vdw_other 0.202 r_nbd_other 0.195 r_nbtor_refined 0.195 r_xyhbond_nbd_refined 0.146 r_symmetry_hbond_refined 0.133 r_nbtor_other 0.089 r_chiral_restr 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3417 Nucleic Acid Atoms Solvent Atoms 475 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling FFT phasing