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Crystal structure of Trypanosome cruzi farnesyl diphosphate synthase in complex with [2-(n-hexylamino)ethane-1,1-diyl]bisphosphonic acid and Mg2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DWG PDB ENTRY 4DWG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 291 PEG4000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.37 48.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.575 α = 90 b = 58.575 β = 90 c = 393.933 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 2011-11-11 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 2.65 65.656 95.7 0.105 12.7 14.2 12287
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 2.65 2.7 99.8 0.473 13.6 612
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 4DWG 2.65 28.969 12120 587 95.1 0.2351 0.2317 0.2282 0.3082 0.2989 RANDOM 51.3117
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] 0.68 0.34 0.68 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.526 r_dihedral_angle_4_deg 18.18 r_dihedral_angle_3_deg 15.737 r_dihedral_angle_1_deg 4.665 r_scangle_it 1.622 r_angle_refined_deg 1.133 r_scbond_it 0.962 r_mcangle_it 0.728 r_mcbond_it 0.383 r_chiral_restr 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.526 r_dihedral_angle_4_deg 18.18 r_dihedral_angle_3_deg 15.737 r_dihedral_angle_1_deg 4.665 r_scangle_it 1.622 r_angle_refined_deg 1.133 r_scbond_it 0.962 r_mcangle_it 0.728 r_mcbond_it 0.383 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2883 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 35
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection DENZO data reduction MOLREP phasing