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Crystal structure of human FPPS in complex with an allosteric inhibitor YF-02037
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, HANGING DROP 6.5 295 1.36M tri-sodium citrate
15% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 2.76 55.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.92 α = 90 b = 110.92 β = 90 c = 77.53 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 MARMOSAIC 300 mm CCD 2018-06-23 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 78.43 99.8 0.043 0.045 0.013 1 25.9 12.9 33080 46.204
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 2.04 99 1.244 1.298 0.365 0.874 2.4 12.4
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 78.43 31318 1704 99.6 0.17377 0.17218 0.1852 0.20442 0.2227 RANDOM 70.04
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] -3.87 -3.87 7.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.306 r_dihedral_angle_4_deg 21.833 r_dihedral_angle_3_deg 16.254 r_long_range_B_refined 9.129 r_long_range_B_other 8.974 r_dihedral_angle_1_deg 6.137 r_scangle_other 5.226 r_scbond_it 3.945 r_mcangle_other 3.819 r_mcangle_it 3.818
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.306 r_dihedral_angle_4_deg 21.833 r_dihedral_angle_3_deg 16.254 r_long_range_B_refined 9.129 r_long_range_B_other 8.974 r_dihedral_angle_1_deg 6.137 r_scangle_other 5.226 r_scbond_it 3.945 r_mcangle_other 3.819 r_mcangle_it 3.818 r_scbond_other 3.789 r_mcbond_it 2.689 r_mcbond_other 2.678 r_angle_refined_deg 1.867 r_angle_other_deg 1.136 r_chiral_restr 0.088 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.004 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 2698 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing