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Crystal structure of human FPPS in ternary complex with YS0470 and inorganic pyrophosphate
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 2.39 48.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.527 α = 90 b = 111.527 β = 90 c = 66.242 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++ 2011-11-14 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 50 100 0.057 59.9 28.2 27996 27996
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 0.484 7.7 27.9 1362
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 26414 26414 1392 99.43 0.18104 0.18104 0.17985 0.1795 0.20302 0.2035 RANDOM 40.725
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] -1.57 -1.57 3.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.5 r_dihedral_angle_4_deg 15.181 r_dihedral_angle_3_deg 14.231 r_dihedral_angle_1_deg 5.209 r_angle_refined_deg 1.885 r_chiral_restr 0.122 r_bond_refined_d 0.019 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2731 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 38
Software Software Software Name Purpose StructureStudio data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing