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Crystal structure of human FPPS in complex with magnesium, CL02134, and inorganic pyrophosphate
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 6.5 295.15 16% PEG8000, 20% glycerol, 0.16 M magnesium acetate, 0.08 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.15K
Crystal Properties Matthews coefficient Solvent content 2.47 50.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.34 α = 90 b = 111.34 β = 90 c = 68.77 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 2013-05-05 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 2.55 50 98.3 0.052 24 9.48 14627 14376
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 2.55 2.62 93.8 0.382 6.07 9.52 1069
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 2.55 35.23 13394 13394 704 96.83 0.20355 0.20355 0.20083 0.204 0.257 0.2492 RANDOM 61.961
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] -6.17 -6.17 12.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.461 r_dihedral_angle_4_deg 19.066 r_dihedral_angle_3_deg 15.073 r_dihedral_angle_1_deg 6.18 r_angle_refined_deg 1.697 r_angle_other_deg 0.851 r_chiral_restr 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.461 r_dihedral_angle_4_deg 19.066 r_dihedral_angle_3_deg 15.073 r_dihedral_angle_1_deg 6.18 r_angle_refined_deg 1.697 r_angle_other_deg 0.851 r_chiral_restr 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2687 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 40
Software Software Software Name Purpose MxDC data collection REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing