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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 2YJ2 PDB ENTRY 2YJ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.1 M BIS-TRIS PH 6.5, 0.2 M NACL, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.75 29.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.365 α = 90 b = 58.495 β = 90 c = 64.042 γ = 90
Symmetry Space Group P 21 21 21
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 2011-02-05 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 1.4 50 95.5 0.1 8.91 5.99 33489 -3 18.66
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 1.4 1.5 91.6 0.66 1.65 5.42
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2YJ2 1.4 46.37 30210 1604 90.89 0.16181 0.15887 0.21779 0.2077 RANDOM 18.053
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] -0.51 -1.89 2.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.197 r_sphericity_free 28.222 r_dihedral_angle_4_deg 13.827 r_dihedral_angle_3_deg 11.716 r_sphericity_bonded 8.548 r_dihedral_angle_1_deg 5.827 r_rigid_bond_restr 2.685 r_angle_refined_deg 1.363 r_angle_other_deg 0.886 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.197 r_sphericity_free 28.222 r_dihedral_angle_4_deg 13.827 r_dihedral_angle_3_deg 11.716 r_sphericity_bonded 8.548 r_dihedral_angle_1_deg 5.827 r_rigid_bond_restr 2.685 r_angle_refined_deg 1.363 r_angle_other_deg 0.886 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 231 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction SADABS data scaling PHASER phasing