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The Crystal Structure of Cruzain in Complex with a Tetrafluorophenoxymethyl Ketone Inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ME3 PDB ENTRY 1ME3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 294 20 % PEG 3000, 100mM sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2 38.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.081 α = 90 b = 51.451 β = 115.5 c = 45.853 γ = 90
Symmetry Space Group P 1 21 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 Vertical focusing mirror; single crystal (Si111) bent monochromator (horizontal focusing). 2008-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.97607 SSRL BL7-1
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 1.2 41.38 97.9 0.062 19.1 6.4 56657 7.81
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) 1.2 1.26 88.7 0.344 6.2 5.7 7468
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 PDB ENTRY 1ME3 1.2 38 53757 2880 97.85 0.12846 0.12713 0.1369 0.15296 0.161 RANDOM 8.137
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] 0.09 0.06 0.37 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.657 r_dihedral_angle_4_deg 18.23 r_sphericity_free 11.557 r_dihedral_angle_3_deg 11.054 r_sphericity_bonded 6.869 r_dihedral_angle_1_deg 6.819 r_scangle_it 4.619 r_scbond_it 3.4 r_mcangle_it 2.761 r_mcbond_it 1.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.657 r_dihedral_angle_4_deg 18.23 r_sphericity_free 11.557 r_dihedral_angle_3_deg 11.054 r_sphericity_bonded 6.869 r_dihedral_angle_1_deg 6.819 r_scangle_it 4.619 r_scbond_it 3.4 r_mcangle_it 2.761 r_mcbond_it 1.95 r_angle_refined_deg 1.907 r_rigid_bond_restr 1.766 r_mcbond_other 1.165 r_angle_other_deg 1.114 r_chiral_restr 0.11 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1663 Nucleic Acid Atoms Solvent Atoms 265 Heterogen Atoms 46
Software Software Software Name Purpose Blu-Ice data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling