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Crystal structure of CfFPPS2, a lepidopteran type-II farnesyl diphosphate synthase, complexed with IPP and [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 3.18 61.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 187.219 α = 90 b = 122.646 β = 107.05 c = 68.145 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 2.6 101.17 99.8 0.107 0.126 0.066 9.7 3.6 44753
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 2.6 2.69 99.6 0.765 0.927 0.517 0.597 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1YV5 2.6 101.17 42494 2258 99.35 0.1867 0.1841 0.1865 0.2349 0.2388 RANDOM 70.508
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] -2.67 -0.37 1.94 0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.602 r_dihedral_angle_3_deg 18.638 r_dihedral_angle_4_deg 13.727 r_dihedral_angle_1_deg 6.389 r_angle_refined_deg 1.818 r_angle_other_deg 1.081 r_chiral_restr 0.094 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.602 r_dihedral_angle_3_deg 18.638 r_dihedral_angle_4_deg 13.727 r_dihedral_angle_1_deg 6.389 r_angle_refined_deg 1.818 r_angle_other_deg 1.081 r_chiral_restr 0.094 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8115 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 102
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction MOLREP phasing