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Crystal structure of unliganded human FPPS at 2.15 angstrom resolution
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 7.5 295.15 17% PEG 4000, 8.5% 2-propanol, 15% glycerol, 0.09 M HEPES
Crystal Properties Matthews coefficient Solvent content 2.78 55.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.85 α = 90 b = 110.85 β = 90 c = 78.08 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 2013-02-13 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) 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 2.15 55.42 99.7 0.082 13.9 9.7 26862
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 2.15 2.21 98.9 0.991 2.5 2.5
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 2F7M 2.15 55.42 25437 1370 99.66 0.18703 0.18502 0.198 0.22475 0.2354 RANDOM 69.975
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] -4.34 -4.34 8.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.525 r_dihedral_angle_4_deg 19.3 r_dihedral_angle_3_deg 16.015 r_long_range_B_refined 7.112 r_long_range_B_other 7.048 r_dihedral_angle_1_deg 6.294 r_scangle_other 5.219 r_mcangle_it 4.358 r_mcangle_other 4.357 r_scbond_other 3.558
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.525 r_dihedral_angle_4_deg 19.3 r_dihedral_angle_3_deg 16.015 r_long_range_B_refined 7.112 r_long_range_B_other 7.048 r_dihedral_angle_1_deg 6.294 r_scangle_other 5.219 r_mcangle_it 4.358 r_mcangle_other 4.357 r_scbond_other 3.558 r_scbond_it 3.557 r_mcbond_it 2.871 r_mcbond_other 2.87 r_angle_refined_deg 1.75 r_angle_other_deg 0.884 r_chiral_restr 0.093 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2664 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing