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Crystal structure of human FPPS in complex with YS0470 and two molecules of inorganic phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H5D PDB ENTRY 4H5D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295.15 30% PEG400, 0.2 M magnesium chloride, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.15K
Crystal Properties Matthews coefficient Solvent content 2.39 48.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.02 α = 90 b = 111.02 β = 90 c = 67.04 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 2012-09-25 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) 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 67.04 99.7 0.07 28.8 14.3 28844 28762 24.5
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 2.05 98.8 0.498 7.4 14.3 2083
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 PDB ENTRY 4H5D 2 51.03 27134 27134 1454 99.28 0.1786 0.1786 0.17646 0.1858 0.21791 0.228 RANDOM 34.973
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] -2.94 -2.94 5.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.488 r_dihedral_angle_4_deg 18.769 r_dihedral_angle_3_deg 14.585 r_long_range_B_refined 7.075 r_long_range_B_other 7.049 r_scangle_other 5.745 r_dihedral_angle_1_deg 5.47 r_scbond_it 3.978 r_scbond_other 3.971 r_mcangle_it 3.836
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.488 r_dihedral_angle_4_deg 18.769 r_dihedral_angle_3_deg 14.585 r_long_range_B_refined 7.075 r_long_range_B_other 7.049 r_scangle_other 5.745 r_dihedral_angle_1_deg 5.47 r_scbond_it 3.978 r_scbond_other 3.971 r_mcangle_it 3.836 r_mcangle_other 3.835 r_mcbond_it 3.09 r_mcbond_other 3.081 r_angle_refined_deg 1.923 r_angle_other_deg 0.895 r_chiral_restr 0.12 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2728 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 40
Software Software Software Name Purpose MxDC data collection REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing