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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 2.72 54.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.968 α = 90 b = 52.881 β = 95.32 c = 80.504 γ = 90
Symmetry Space Group P 1 21 1
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 2.29 35.06 98.8 22027
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 2.29 35.06 22027 1191 98.8 0.18 0.178 0.1825 0.217 0.2205 RANDOM 26.14
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] 0.08 -0.06 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.596 r_dihedral_angle_4_deg 17.713 r_dihedral_angle_3_deg 14.281 r_dihedral_angle_1_deg 5.802 r_long_range_B_refined 4.523 r_long_range_B_other 4.335 r_scangle_other 2.652 r_mcangle_it 1.898 r_mcangle_other 1.898 r_scbond_it 1.596
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.596 r_dihedral_angle_4_deg 17.713 r_dihedral_angle_3_deg 14.281 r_dihedral_angle_1_deg 5.802 r_long_range_B_refined 4.523 r_long_range_B_other 4.335 r_scangle_other 2.652 r_mcangle_it 1.898 r_mcangle_other 1.898 r_scbond_it 1.596 r_scbond_other 1.594 r_angle_refined_deg 1.258 r_mcbond_it 1.159 r_mcbond_other 1.156 r_angle_other_deg 0.922 r_chiral_restr 0.076 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 3377 Nucleic Acid Atoms Solvent Atoms 355 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling