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Crystal Structure of Cathepsin S in complex with a Nonpeptidic Inhibitor (Hexagonal spacegroup)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H7J pdb entry 2H7J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 277 1.0M Lithium Chloride, 30% PEG 6000, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.86 68.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 165.928 α = 90 b = 165.928 β = 90 c = 142.082 γ = 120
Symmetry Space Group P 65 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 4 2005-07-25 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 1.9 80 99.7 0.089 0.059 23.67 5.8 90365 90365
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) 1.9 1.97 100 0.747 0.747 2.12 5.8 8924
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 2H7J 1.9 84.51 90365 90365 6833 98.9 0.22005 0.21907 0.2384 RANDOM 23.144
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] 1.39 0.69 1.39 -2.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.097 r_dihedral_angle_4_deg 16.275 r_dihedral_angle_3_deg 11.832 r_dihedral_angle_1_deg 6.984 r_scangle_it 2.235 r_scbond_it 1.584 r_angle_refined_deg 1.32 r_angle_other_deg 1.075 r_mcangle_it 0.939 r_mcbond_it 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.097 r_dihedral_angle_4_deg 16.275 r_dihedral_angle_3_deg 11.832 r_dihedral_angle_1_deg 6.984 r_scangle_it 2.235 r_scbond_it 1.584 r_angle_refined_deg 1.32 r_angle_other_deg 1.075 r_mcangle_it 0.939 r_mcbond_it 0.82 r_symmetry_vdw_other 0.244 r_symmetry_hbond_refined 0.204 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.189 r_nbtor_refined 0.188 r_nbd_other 0.187 r_xyhbond_nbd_refined 0.142 r_mcbond_other 0.124 r_nbtor_other 0.085 r_chiral_restr 0.073 r_bond_refined_d 0.014 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5110 Nucleic Acid Atoms Solvent Atoms 665 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing