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Crystal structure analysis of cruzain with three Fragments: 1 (N-(1H-benzimidazol-2-yl)-1,3-dimethyl-pyrazole-4-carboxamide), 6 (2-amino-4,6-difluorobenzothiazole) and 9 (N-(1H-benzimidazol-2-yl)-3-(4-fluorophenyl)-1H-pyrazole-4-carboxamide).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KKU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1M Hepes pH 7.5, 1.2M K/Na Tartrate
Crystal Properties Matthews coefficient Solvent content 3.47 64.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.79 α = 90 b = 137.79 β = 90 c = 166.48 γ = 90
Symmetry Space Group P 43 21 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 315r 2012-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.115 ALS 8.3.1
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 3.27 30 98.4 0.08 17.8 8.1 25366 84.44
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3KKU 3.27 29.98 1.99 25279 1013 99.6 0.195 0.193 0.1958 0.236 0.2392 86.96
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.614 f_angle_d 1.255 f_chiral_restr 0.079 f_bond_d 0.01 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7956 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 98
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction XSCALE data scaling XDS data reduction SCALA data scaling