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Crystal structure of CfFPPS2, a lepidopteran type-II farnesyl diphosphate synthase, complexed with [1-phosphono-2-(1-propylpyridin-2-yl)ethyl]phosphonic acid (inhibitor 1d)
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 sodium formate
Crystal Properties Matthews coefficient Solvent content 3.23 61.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 186.913 α = 90 b = 122.579 β = 106.51 c = 69.064 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 RIGAKU SATURN 944 2015-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 1.98 101.18 96 0.069 0.08 0.041 9.3 3.7 99585
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 1.98 2.05 82 0.536 0.643 0.351 0.735 3.1
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 1.98 101.18 94476 4966 95.86 0.1728 0.1709 0.1796 0.2089 0.2154 RANDOM 32.884
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] 0.33 -0.13 -0.42 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.434 r_dihedral_angle_4_deg 19.77 r_dihedral_angle_3_deg 15.129 r_dihedral_angle_1_deg 5.562 r_angle_refined_deg 1.915 r_angle_other_deg 1.15 r_chiral_restr 0.134 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.434 r_dihedral_angle_4_deg 19.77 r_dihedral_angle_3_deg 15.129 r_dihedral_angle_1_deg 5.562 r_angle_refined_deg 1.915 r_angle_other_deg 1.15 r_chiral_restr 0.134 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8148 Nucleic Acid Atoms Solvent Atoms 911 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction DENZO data reduction MOLREP phasing