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Crystal structure of human FPPS in complex with an allosteric inhibitor CL-08-038
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 0.85 M lithium sulfate, 0.425 M ammonium sulfate, 15% glycerol, 0.085 M tri-sodium citrate, pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.74 55.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.54 α = 90 b = 111.54 β = 90 c = 75.98 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+ 2015-04-07 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 2.4 41.7 88.4 0.064 31.9 12.1 17150 36.381
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 2.4 2.46 52.4 0.713 2.1 5.1
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 FOURIER SYNTHESIS THROUGHOUT 4QXS 2.4 41.7 16251 863 88.24 0.17936 0.17636 0.1859 0.23504 0.2403 RANDOM 56.403
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] -3.41 -3.41 6.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.168 r_dihedral_angle_4_deg 22.924 r_dihedral_angle_3_deg 16.397 r_long_range_B_refined 7.672 r_long_range_B_other 7.672 r_dihedral_angle_1_deg 6.671 r_scangle_other 3.665 r_mcangle_other 2.492 r_mcangle_it 2.49 r_scbond_it 2.437
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.168 r_dihedral_angle_4_deg 22.924 r_dihedral_angle_3_deg 16.397 r_long_range_B_refined 7.672 r_long_range_B_other 7.672 r_dihedral_angle_1_deg 6.671 r_scangle_other 3.665 r_mcangle_other 2.492 r_mcangle_it 2.49 r_scbond_it 2.437 r_scbond_other 2.437 r_angle_refined_deg 2.132 r_mcbond_it 1.533 r_mcbond_other 1.524 r_angle_other_deg 1.191 r_chiral_restr 0.116 r_bond_refined_d 0.022 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 2701 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing