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Crystal structure analysis of cruzain with Fragment 1 (N-(1H-benzimidazol-2-yl)-1,3-dimethyl-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 293 0.1 M Tris pH 8.0 and 1.6 M of Na/K Tartrate
Crystal Properties Matthews coefficient Solvent content 3.79 67.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.1 α = 90 b = 137.1 β = 90 c = 109.8 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 2013-02-10 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) 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 2.7 30 99.8 14 8.8 29319 29249 29.26
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 2.701 29.527 2 29230 1170 99.86 0.214 0.2123 0.2165 0.2544 0.2548 40.4351
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 13.668 f_angle_d 1.191 f_chiral_restr 0.053 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4776 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 57
Software Software Software Name Purpose MOSFLM data reduction PDB_EXTRACT data extraction XSCALE data scaling PHENIX refinement