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CATHEPSIN L WITH A NITRILE INHIBITOR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HWN PDB ENTRY 3HWN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.2 0.1 M CITRIC ACID PH 3.5 25 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.93 36.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.441 α = 90 b = 49.394 β = 105.13 c = 46.129 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 PIXEL DECTRIS PILATUS 6M 2010-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 0.9 50 98.1 0.08 8.11 3.32 139614 -3 9.15
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.9 1 96.5 0.64 1.25 3.19
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 3HWN 0.9 44.53 125923 6706 93.19 0.14248 0.14183 0.1493 0.15473 0.1609 RANDOM 8.362
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] 0.2 0.19 0.07 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.097 r_dihedral_angle_4_deg 17.323 r_dihedral_angle_3_deg 11.067 r_sphericity_free 7.963 r_dihedral_angle_1_deg 5.914 r_rigid_bond_restr 4.626 r_sphericity_bonded 2.938 r_angle_refined_deg 1.556 r_angle_other_deg 0.878 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.097 r_dihedral_angle_4_deg 17.323 r_dihedral_angle_3_deg 11.067 r_sphericity_free 7.963 r_dihedral_angle_1_deg 5.914 r_rigid_bond_restr 4.626 r_sphericity_bonded 2.938 r_angle_refined_deg 1.556 r_angle_other_deg 0.878 r_chiral_restr 0.101 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1697 Nucleic Acid Atoms Solvent Atoms 373 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement XDS data reduction SADABS data scaling PHASER phasing