☰ Navigation Tabs
Crystal structure of human FPPS in complex with an allosteric inhibitor YF-02-82
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 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 2.76 55.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.35 α = 90 b = 111.35 β = 90 c = 76.86 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 2019-02-25 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 2.3 76.86 99.6 0.067 0.069 0.02 1 18.8 12.7 21951 55.395
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 2.3 2.34 97.3 1.631 1.707 0.496 0.797 1.7 11.5
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 2.3 55.74 20856 1047 99.35 0.19569 0.1934 0.2054 0.24145 0.2535 RANDOM 80.074
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] -4.41 -4.41 8.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.838 r_dihedral_angle_4_deg 18.8 r_dihedral_angle_3_deg 16.492 r_long_range_B_refined 10.009 r_long_range_B_other 9.933 r_dihedral_angle_1_deg 6.8 r_scangle_other 4.18 r_mcangle_it 3.473 r_mcangle_other 3.472 r_scbond_it 2.621
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.838 r_dihedral_angle_4_deg 18.8 r_dihedral_angle_3_deg 16.492 r_long_range_B_refined 10.009 r_long_range_B_other 9.933 r_dihedral_angle_1_deg 6.8 r_scangle_other 4.18 r_mcangle_it 3.473 r_mcangle_other 3.472 r_scbond_it 2.621 r_scbond_other 2.607 r_mcbond_it 2.251 r_mcbond_other 2.251 r_angle_refined_deg 1.685 r_angle_other_deg 1.422 r_chiral_restr 0.068 r_bond_refined_d 0.018 r_bond_other_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.004 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 2700 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing