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Crystal structure of Trypanosome cruzi farnesyl diphosphate synthase in complex with [2-(n-propylamino)ethane-1,1-diyl]bisphosphonic acid and Mg2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YHM PDB ENTRY 1YHM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 291 12.5 mg/mL protein in 250 uM inhibitor, 250 uM IPP, 1 mM magnesium chloride, mother liquor: 100 mM sodium acetate, pH 4.6-5.2, 200 mM ammonium sulfate, 2-10% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.4 48.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.22 α = 90 b = 103.22 β = 90 c = 386.658 γ = 120
Symmetry Space Group P 61 2 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 210 2011-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 0.979 NSLS X6A
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 2.35 89.391 96 0.09 9.5 9.1 49874
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 2.35 2.39 93.7 0.52 6.8 2346
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1YHM 2.35 38.722 49345 2519 95.23 0.2228 0.2195 0.2163 0.2853 0.2807 RANDOM 40.287
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] 1.12 0.56 1.12 -1.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.916 r_dihedral_angle_4_deg 19.456 r_dihedral_angle_3_deg 17.148 r_dihedral_angle_1_deg 4.773 r_scangle_it 2.131 r_scbond_it 1.341 r_angle_refined_deg 1.208 r_mcangle_it 0.793 r_mcbond_it 0.404 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.916 r_dihedral_angle_4_deg 19.456 r_dihedral_angle_3_deg 17.148 r_dihedral_angle_1_deg 4.773 r_scangle_it 2.131 r_scbond_it 1.341 r_angle_refined_deg 1.208 r_mcangle_it 0.793 r_mcbond_it 0.404 r_chiral_restr 0.089 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8673 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 152
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection DENZO data reduction REFMAC phasing