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Crystal structure of human Cathepsin-S with bound ligand
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 100MM SODIUM ACETATE PH 4.5, 200MM AMMONIUM ACETATE, 25% PEG 8000. PROTEIN CONCENTRATION 7 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 2.07 40.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.98 α = 70.92 b = 52.93 β = 72.06 c = 58.46 γ = 73.46
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 RIGAKU SATURN 944 2006-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 53.67 79.2 23098
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 MOLECULAR REPLACEMENT THROUGHOUT 1.9 53.67 23098 1246 79.2 0.215 0.213 0.2191 0.257 0.2611 RANDOM 28.89
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] -0.49 0.12 -0.2 0.4 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.803 r_dihedral_angle_4_deg 24.242 r_dihedral_angle_3_deg 13.562 r_dihedral_angle_1_deg 5.587 r_long_range_B_refined 3.932 r_long_range_B_other 3.783 r_scangle_other 2.577 r_mcangle_other 2.03 r_mcangle_it 2.027 r_scbond_it 1.624
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.803 r_dihedral_angle_4_deg 24.242 r_dihedral_angle_3_deg 13.562 r_dihedral_angle_1_deg 5.587 r_long_range_B_refined 3.932 r_long_range_B_other 3.783 r_scangle_other 2.577 r_mcangle_other 2.03 r_mcangle_it 2.027 r_scbond_it 1.624 r_scbond_other 1.622 r_mcbond_it 1.323 r_angle_refined_deg 1.317 r_mcbond_other 1.309 r_angle_other_deg 0.922 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 3400 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling