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Crystal structure of human FPPS in complex with magnesium, JDS05120, and sulfate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DEM PDB ENTRY 4DEM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 295 25.5% PEG MME 2000, 0.17M ammonium sulfate, 15% glycerol, 0.09M sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.43 49.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.235 α = 90 b = 111.235 β = 90 c = 67.919 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 2013-02-20 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 2.05 50 99.4 0.06 31.3 9.5 27177 27177
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 2.05 2.09 98.6 0.472 4 9.3 1311
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 4DEM 2.05 50 25777 25777 1360 99.44 0.17549 0.17549 0.1735 0.2125 0.2314 RANDOM 46.148
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] -2.7 -2.7 5.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.057 r_dihedral_angle_4_deg 18.77 r_dihedral_angle_3_deg 14.949 r_long_range_B_refined 6.274 r_long_range_B_other 6.274 r_dihedral_angle_1_deg 5.393 r_scangle_other 4.642 r_scbond_it 3.075 r_scbond_other 3.074 r_mcangle_it 2.805
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.057 r_dihedral_angle_4_deg 18.77 r_dihedral_angle_3_deg 14.949 r_long_range_B_refined 6.274 r_long_range_B_other 6.274 r_dihedral_angle_1_deg 5.393 r_scangle_other 4.642 r_scbond_it 3.075 r_scbond_other 3.074 r_mcangle_it 2.805 r_mcangle_other 2.804 r_mcbond_it 2.078 r_mcbond_other 2.071 r_angle_refined_deg 1.891 r_angle_other_deg 0.95 r_chiral_restr 0.11 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2709 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 34
Software Software Software Name Purpose MxDC data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing