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Crystal Structure of Leshmaniasis major Farnesyl diphosphate synthase in complex with 3-BUTYL-1-(2,2-DIPHOSPHONOETHYL)PYRIDINIUM, IPP and Ca2+
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 6.5 291 PEG 3350, pH 6.5, hanging drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.25 45.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.428 α = 90 b = 85.805 β = 90 c = 106.867 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS 2009-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.54178
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 1.8 50 99.8 0.07 10.6 6.8 68699
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 1.8 1.86 99.9 0.545 5.4 6788
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.8 25.94 68610 3477 99.78 0.1807 0.1782 0.2272 0.2129 RANDOM 28.0746
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] 0.9 -0.56 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.669 r_dihedral_angle_3_deg 12.363 r_dihedral_angle_4_deg 10.421 r_dihedral_angle_1_deg 4.286 r_scangle_it 2.317 r_scbond_it 1.472 r_angle_refined_deg 1.108 r_mcangle_it 0.858 r_mcbond_it 0.556 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.669 r_dihedral_angle_3_deg 12.363 r_dihedral_angle_4_deg 10.421 r_dihedral_angle_1_deg 4.286 r_scangle_it 2.317 r_scbond_it 1.472 r_angle_refined_deg 1.108 r_mcangle_it 0.858 r_mcbond_it 0.556 r_nbtor_refined 0.3 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.134 r_symmetry_hbond_refined 0.133 r_metal_ion_refined 0.12 r_xyhbond_nbd_refined 0.113 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5752 Nucleic Acid Atoms Solvent Atoms 776 Heterogen Atoms 74
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection