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Crystal structure analysis of cruzain bound to vinyl sulfone analog of WRR-483 (WRR-666)
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 6.5 293 0.2 M Magnesium acetate, 30% (+/-)-2-Methyl-2,4-Pentanediol and 0.1 M Sodium cacodylate
Crystal Properties Matthews coefficient Solvent content 2.46 49.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.923 α = 90 b = 38.669 β = 113.91 c = 94.646 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 315r 2011-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1159 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 1.27 63.62 99.1 0.085 8.7 5.2 114913
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 3KKU 1.27 86.52 109411 5804 98.25 0.17507 0.17391 0.1737 0.19741 0.1962 RANDOM 17.982
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] -0.75 -0.16 1.41 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.977 r_dihedral_angle_4_deg 20.737 r_dihedral_angle_3_deg 10.353 r_dihedral_angle_1_deg 6.596 r_angle_refined_deg 2.506 r_chiral_restr 0.163 r_bond_refined_d 0.027 r_gen_planes_refined 0.015 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.977 r_dihedral_angle_4_deg 20.737 r_dihedral_angle_3_deg 10.353 r_dihedral_angle_1_deg 6.596 r_angle_refined_deg 2.506 r_chiral_restr 0.163 r_bond_refined_d 0.027 r_gen_planes_refined 0.015 r_bond_other_d r_angle_other_deg r_gen_planes_other 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3184 Nucleic Acid Atoms Solvent Atoms 459 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction