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Structure of the complex of Trypanosoma cruzi farnesyl disphosphate synthase with alendronate, Isopentenyl diphosphate and mg+2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YHK PDB ENTRY 1YHK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 4.6 293 peg 4000 Na acetate amonium sulfate, pH 4.6, LIQUID DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 48.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.205 α = 90 b = 103.205 β = 90 c = 385.236 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 315 2004-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
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 2.3 87.71 0.146 12.9 55148
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 2.3 2.38 95.6 0.895 6.3
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1YHK 2.5 87.71 40998 2189 99.86 0.2114 0.20798 0.2777 RANDOM 42.193
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] 1.5 0.75 1.5 -2.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.897 r_dihedral_angle_4_deg 23.692 r_dihedral_angle_3_deg 19.417 r_dihedral_angle_1_deg 6.06 r_scangle_it 3.93 r_scbond_it 2.91 r_angle_refined_deg 1.981 r_mcbond_it 1.509 r_mcangle_it 1.397 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.897 r_dihedral_angle_4_deg 23.692 r_dihedral_angle_3_deg 19.417 r_dihedral_angle_1_deg 6.06 r_scangle_it 3.93 r_scbond_it 2.91 r_angle_refined_deg 1.981 r_mcbond_it 1.509 r_mcangle_it 1.397 r_nbtor_refined 0.32 r_symmetry_vdw_refined 0.273 r_nbd_refined 0.25 r_chiral_restr 0.182 r_xyhbond_nbd_refined 0.176 r_metal_ion_refined 0.153 r_symmetry_hbond_refined 0.104 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8673 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 108
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction AMoRE phasing