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Crystal structure of human FPPS in ternary complex with YS0470 and inorganic phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DEM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 295 30% PEG 300, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal Properties Matthews coefficient Solvent content 2.38 48.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.979 α = 90 b = 110.979 β = 90 c = 66.785 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 IMAGE PLATE RIGAKU RAXIS IV++ 2011-01-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
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 2.02 50 99.9 0.077 36.9 26.4 28025 28025
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 2.02 2.05 100 0.569 5.7 24.1 1369
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 4DEM 2.02 50 26374 26374 1401 98.76 0.1816 0.1816 0.18 0.1814 0.21317 0.2183 RANDOM 41.231
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] -2.45 -2.45 4.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.303 r_dihedral_angle_4_deg 16.697 r_dihedral_angle_3_deg 14.445 r_dihedral_angle_1_deg 5.438 r_angle_refined_deg 1.843 r_chiral_restr 0.126 r_bond_refined_d 0.018 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2689 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 34
Software Software Software Name Purpose StructureStudio data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing