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Crystal structure of human FPPS in complex with an allosteric inhibitor YF-02-78
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H5C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 0.075 M HEPES, 0.6 M potassium phosphate, 0.6 M sodium phosphate, 25% glycerol
Crystal Properties Matthews coefficient Solvent content 2.51 51.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.33 α = 90 b = 111.33 β = 90 c = 70 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2019-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.2 78.72 99.5 0.066 0.069 0.019 1 19.6 12.9 22715 48.072
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 2.2 2.24 98.6 1.65 1.718 0.475 0.48 1.7 12.8
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 FOURIER SYNTHESIS THROUGHOUT 4H5C 2.2 78.72 21448 1215 99.27 0.21046 0.20761 0.2307 0.26041 0.2827 RANDOM 71.491
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] -6.19 -6.19 12.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.736 r_dihedral_angle_3_deg 17.72 r_dihedral_angle_4_deg 16.418 r_long_range_B_refined 7.106 r_long_range_B_other 6.968 r_dihedral_angle_1_deg 6.692 r_scangle_other 4.101 r_mcangle_other 3.322 r_mcangle_it 3.321 r_scbond_it 2.643
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.736 r_dihedral_angle_3_deg 17.72 r_dihedral_angle_4_deg 16.418 r_long_range_B_refined 7.106 r_long_range_B_other 6.968 r_dihedral_angle_1_deg 6.692 r_scangle_other 4.101 r_mcangle_other 3.322 r_mcangle_it 3.321 r_scbond_it 2.643 r_scbond_other 2.589 r_mcbond_it 2.192 r_mcbond_other 2.19 r_angle_refined_deg 1.667 r_angle_other_deg 1.374 r_chiral_restr 0.071 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2716 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing