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Crystal structure of cathepsin L in complex with AZ12878478
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.4 293 PEG, pH 7.4, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.16 43.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.26 α = 105.6 b = 62.69 β = 93.22 c = 68.24 γ = 115.55
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 PSI PILATUS 6M LN2 cooled fixed-exit 2007-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0000 SLS X06SA
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 1.27 44.28 85.6 0.034 1.5 182842 182842
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 1.27 1.33 65.8 0.098 0.4
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 (All) 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 FOURIER SYNTHESIS THROUGHOUT 1.27 44.28 173697 9143 100 0.11672 0.11812 0.11632 0.1182 0.15237 0.1537 RANDOM 12.158
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] -0.34 -0.25 -0.05 0.26 -0.6 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.701 r_sphericity_free 12.266 r_dihedral_angle_4_deg 11.519 r_dihedral_angle_3_deg 11.187 r_sphericity_bonded 6.143 r_dihedral_angle_1_deg 5.89 r_scangle_it 5.842 r_scbond_it 4.779 r_mcangle_it 3.528 r_mcbond_it 3.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.701 r_sphericity_free 12.266 r_dihedral_angle_4_deg 11.519 r_dihedral_angle_3_deg 11.187 r_sphericity_bonded 6.143 r_dihedral_angle_1_deg 5.89 r_scangle_it 5.842 r_scbond_it 4.779 r_mcangle_it 3.528 r_mcbond_it 3.102 r_rigid_bond_restr 2.449 r_mcbond_other 1.798 r_angle_refined_deg 1.355 r_angle_other_deg 0.81 r_symmetry_hbond_refined 0.369 r_symmetry_vdw_other 0.269 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.204 r_nbd_other 0.19 r_symmetry_vdw_refined 0.189 r_nbtor_refined 0.185 r_chiral_restr 0.089 r_nbtor_other 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6695 Nucleic Acid Atoms Solvent Atoms 993 Heterogen Atoms 145
Software Software Software Name Purpose XDL data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling