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Crystal Structure of Cathepsin S in complex with a Zinc mediated non-covalent arylaminoethyl amide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F1G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 0.2M ZnAcetate, 20% PEG-3350, 150mM Sodium Chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.33 47.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.542 α = 90 b = 109.542 β = 90 c = 98.529 γ = 120
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 4 2003-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 1.0 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 1.8 34.2 99.3 0.064 0.064 17.7 2.7 38549 38549
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) 1.8 1.86 98.2 0.763 0.763 1.3 2.5 4514
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 MOLECULAR REPLACEMENT THROUGHOUT 2F1G 1.8 34.2 38549 38549 2048 99.34 0.1757 0.17567 0.17328 0.22015 RANDOM 27.905
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] -0.72 -0.36 -0.72 1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.744 r_dihedral_angle_4_deg 12.584 r_dihedral_angle_3_deg 12.197 r_dihedral_angle_1_deg 6.018 r_scangle_it 4.303 r_scbond_it 3.349 r_mcangle_it 1.713 r_angle_refined_deg 1.511 r_mcbond_it 1.425 r_angle_other_deg 0.765
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.744 r_dihedral_angle_4_deg 12.584 r_dihedral_angle_3_deg 12.197 r_dihedral_angle_1_deg 6.018 r_scangle_it 4.303 r_scbond_it 3.349 r_mcangle_it 1.713 r_angle_refined_deg 1.511 r_mcbond_it 1.425 r_angle_other_deg 0.765 r_mcbond_other 0.3 r_symmetry_vdw_refined 0.283 r_symmetry_vdw_other 0.234 r_nbd_refined 0.201 r_nbtor_refined 0.191 r_nbd_other 0.18 r_symmetry_hbond_refined 0.166 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.134 r_metal_ion_refined 0.114 r_symmetry_metal_ion_refined 0.109 r_nbtor_other 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3372 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement PROCESS data reduction HKL-2000 data scaling MOLREP phasing