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Crystal Structure of Leshmaniasis major Farnesyl diphosphate synthase in complex with 1-(2-HYDROXY-2,2-DIPHOSPHONOETHYL)-3-PHENYLPYRIDINIUM, IPP and Ca2+
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.25 45.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.361 α = 90 b = 85.967 β = 90 c = 107.074 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 2009-07-22 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 1.9 66.96 99.4 0.072 11.5 6.8 58810
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 1.9 1.97 95.3 0.473 4.1 5551
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.9 66.96 58732 2971 99.35 0.1746 0.1727 0.1722 0.2097 0.2073 RANDOM 23.043
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] 0.72 -0.67 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.973 r_dihedral_angle_3_deg 12.503 r_dihedral_angle_4_deg 9.251 r_dihedral_angle_1_deg 4.298 r_scangle_it 2.667 r_scbond_it 1.71 r_mcangle_it 1.181 r_angle_refined_deg 1.076 r_mcbond_it 0.6 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.973 r_dihedral_angle_3_deg 12.503 r_dihedral_angle_4_deg 9.251 r_dihedral_angle_1_deg 4.298 r_scangle_it 2.667 r_scbond_it 1.71 r_mcangle_it 1.181 r_angle_refined_deg 1.076 r_mcbond_it 0.6 r_nbtor_refined 0.298 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.165 r_metal_ion_refined 0.162 r_xyhbond_nbd_refined 0.116 r_symmetry_hbond_refined 0.115 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5752 Nucleic Acid Atoms Solvent Atoms 696 Heterogen Atoms 82
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection AMoRE phasing