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Crystal Structure of Cathepsin S in complex with a Nonpeptidic Inhibitor.
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 5 277 30% Peg-6000, 0.1M Lithium Chloride in Citrate Buffer pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.8 56.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.222 α = 90 b = 85.222 β = 90 c = 150.754 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 2005-07-25 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 1.5 38.6 99.3 0.073 0.073 27.4 92453 92453
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) 1.5 1.53 95.3 0.642 0.642 2.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2f1g 1.5 38.6 84345 84345 4508 99.42 0.16235 0.16143 0.1702 0.17969 0.1862 RANDOM 12.293
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] 0.11 0.11 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.936 r_dihedral_angle_4_deg 13.527 r_dihedral_angle_3_deg 10.392 r_dihedral_angle_1_deg 5.377 r_scangle_it 2.729 r_scbond_it 1.731 r_angle_refined_deg 1.331 r_mcangle_it 1.081 r_angle_other_deg 0.723 r_mcbond_it 0.699
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.936 r_dihedral_angle_4_deg 13.527 r_dihedral_angle_3_deg 10.392 r_dihedral_angle_1_deg 5.377 r_scangle_it 2.729 r_scbond_it 1.731 r_angle_refined_deg 1.331 r_mcangle_it 1.081 r_angle_other_deg 0.723 r_mcbond_it 0.699 r_xyhbond_nbd_refined 0.263 r_symmetry_vdw_refined 0.21 r_nbd_refined 0.2 r_symmetry_vdw_other 0.192 r_nbtor_refined 0.191 r_nbd_other 0.177 r_symmetry_hbond_refined 0.166 r_mcbond_other 0.141 r_nbtor_other 0.083 r_chiral_restr 0.067 r_bond_refined_d 0.015 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3429 Nucleic Acid Atoms Solvent Atoms 549 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement ADSC data collection CCP4 data scaling