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Crystal structure of human FPPS in complex with an allosteric inhibitor MIT-01-055
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QXS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 1.6 M ammonium phosphate, 20% glycerol, 0.08 M TrisHCl, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.69 54.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.41 α = 90 b = 110.41 β = 90 c = 76.27 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+ 2016-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.3 55.21 99 0.048 44.2 17 21337 37.923
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.36 98.8 0.972 2.6 11.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 4QXS 2.3 55.21 20190 1106 98.99 0.18894 0.18623 0.23658 0.2018 RANDOM 59.844
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] -3.17 -3.17 6.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.446 r_dihedral_angle_4_deg 18.709 r_dihedral_angle_3_deg 16.267 r_long_range_B_refined 8.196 r_long_range_B_other 8.195 r_dihedral_angle_1_deg 6.133 r_scangle_other 4.399 r_scbond_it 2.809 r_scbond_other 2.808 r_mcangle_it 2.759
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.446 r_dihedral_angle_4_deg 18.709 r_dihedral_angle_3_deg 16.267 r_long_range_B_refined 8.196 r_long_range_B_other 8.195 r_dihedral_angle_1_deg 6.133 r_scangle_other 4.399 r_scbond_it 2.809 r_scbond_other 2.808 r_mcangle_it 2.759 r_mcangle_other 2.759 r_angle_refined_deg 2.157 r_mcbond_it 1.818 r_mcbond_other 1.805 r_angle_other_deg 1.179 r_chiral_restr 0.122 r_bond_refined_d 0.024 r_gen_planes_refined 0.011 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 2602 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing