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Crystal structure of CfFPPS2, a lepidopteran type-II farnesyl diphosphate synthase, complexed with [2-(1-methylpyridin-2-yl)-1-phosphono-ethyl]phosphonic acid (inhibitor 1b)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YV5 PDB entry 1YV5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 295 20% PEG3350, 0.2 M ammonium formate
Crystal Properties Matthews coefficient Solvent content 3.22 61.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 187.44 α = 90 b = 122.449 β = 106.6 c = 68.761 γ = 90
Symmetry Space Group C 1 2 1
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 RAYONIX MX-300 2015-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9795 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.82 101.18 100 0.057 0.067 0.034 12.8 3.8 131301
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 1.89 100 0.704 0.82 0.419 0.65 3.8
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1YV5 1.83 101.18 124696 6604 99.68 0.1583 0.1566 0.1665 0.1908 0.1984 RANDOM 33.66
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] -0.18 -0.05 -0.13 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.332 r_dihedral_angle_4_deg 16.371 r_dihedral_angle_3_deg 14.978 r_dihedral_angle_1_deg 5.448 r_angle_refined_deg 2.061 r_angle_other_deg 1.145 r_chiral_restr 0.15 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.332 r_dihedral_angle_4_deg 16.371 r_dihedral_angle_3_deg 14.978 r_dihedral_angle_1_deg 5.448 r_angle_refined_deg 2.061 r_angle_other_deg 1.145 r_chiral_restr 0.15 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8157 Nucleic Acid Atoms Solvent Atoms 911 Heterogen Atoms 80
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction MOLREP phasing