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Crystal structure of human FPPS in complex with an allosteric inhibitor AM-02-072
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XQR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295.15 0.6 M sodium phosphate, 0.6 M potassium phosphate, 25% glycerol, 0.075 M HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.66 53.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.48 α = 90 b = 110.48 β = 90 c = 75.2 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 CCD RIGAKU SATURN 944+ 2015-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.65 55.24 99.8 0.085 0.999 26.7 12.5 14007 41.62
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.72 98 1.037 0.748 1.9 7.7
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 4XQR 2.65 55.24 13266 702 99.76 0.17451 0.17096 0.1809 0.24291 0.2422 RANDOM 62.585
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] -3.5 -3.5 6.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.263 r_dihedral_angle_4_deg 20.567 r_dihedral_angle_3_deg 16.351 r_long_range_B_refined 6.508 r_long_range_B_other 6.507 r_dihedral_angle_1_deg 6.364 r_scangle_other 3.978 r_mcangle_it 2.706 r_mcangle_other 2.705 r_scbond_it 2.643
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.263 r_dihedral_angle_4_deg 20.567 r_dihedral_angle_3_deg 16.351 r_long_range_B_refined 6.508 r_long_range_B_other 6.507 r_dihedral_angle_1_deg 6.364 r_scangle_other 3.978 r_mcangle_it 2.706 r_mcangle_other 2.705 r_scbond_it 2.643 r_scbond_other 2.642 r_angle_refined_deg 2.075 r_mcbond_it 1.734 r_mcbond_other 1.677 r_angle_other_deg 1.174 r_chiral_restr 0.105 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d 0.003 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 2683 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing