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Crystal structure of human FPPS with allosterically bound FPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F7M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 295.15 0.08 M TrisHCl, 1.6 M ammonium phosphate, 20% glycerol
Crystal Properties Matthews coefficient Solvent content 2.76 55.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.89 α = 90 b = 110.89 β = 90 c = 77.48 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 RAYONIX MX-300 2014-09-19 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) 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 1.9 49.59 99.8 0.039 0.1 31.5 9.7 38509 36.118
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 1.9 1.95 99 1.111 2.4 9.7
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 2F7M 1.9 49.59 36427 2025 99.75 0.17401 0.17201 0.1865 0.2108 0.2287 RANDOM 53.974
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] -2.62 -2.62 5.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.875 r_dihedral_angle_4_deg 15.389 r_dihedral_angle_3_deg 14.515 r_long_range_B_refined 7.591 r_long_range_B_other 7.591 r_dihedral_angle_1_deg 5.58 r_scangle_other 4.723 r_scbond_it 3.203 r_scbond_other 3.202 r_mcangle_other 2.943
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.875 r_dihedral_angle_4_deg 15.389 r_dihedral_angle_3_deg 14.515 r_long_range_B_refined 7.591 r_long_range_B_other 7.591 r_dihedral_angle_1_deg 5.58 r_scangle_other 4.723 r_scbond_it 3.203 r_scbond_other 3.202 r_mcangle_other 2.943 r_mcangle_it 2.942 r_angle_refined_deg 2.403 r_mcbond_it 2.152 r_mcbond_other 2.151 r_angle_other_deg 1.246 r_chiral_restr 0.159 r_bond_refined_d 0.029 r_gen_planes_refined 0.014 r_bond_other_d 0.002 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 2595 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing