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Crystal structure of human FPPS in complex with WC01088
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F7M PDB ENTRY 2F7M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 295 1.6 M ammonium phosphate, 20% glycerol, 0.08 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.76 55.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.65 α = 90 b = 110.65 β = 90 c = 77.92 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 2014-07-08 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 1.9 55.21 99.4 0.041 28.2 9.7 38434 38434 36.5
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 1.9 1.95 98.6 1.177 2.9 9.6 2768
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 2F7M 1.9 55.21 36355 36355 2023 99.27 0.17145 0.17145 0.16952 0.1782 0.20649 0.2145 RANDOM 59.447
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] -3.38 -3.38 6.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.531 r_dihedral_angle_4_deg 17.022 r_dihedral_angle_3_deg 14.84 r_long_range_B_refined 8.145 r_long_range_B_other 8.144 r_dihedral_angle_1_deg 5.891 r_scangle_other 5.599 r_mcangle_other 4.004 r_mcangle_it 4.002 r_scbond_it 3.895
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.531 r_dihedral_angle_4_deg 17.022 r_dihedral_angle_3_deg 14.84 r_long_range_B_refined 8.145 r_long_range_B_other 8.144 r_dihedral_angle_1_deg 5.891 r_scangle_other 5.599 r_mcangle_other 4.004 r_mcangle_it 4.002 r_scbond_it 3.895 r_scbond_other 3.892 r_mcbond_it 2.769 r_mcbond_other 2.753 r_angle_refined_deg 1.866 r_angle_other_deg 0.907 r_chiral_restr 0.104 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2674 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 46
Software Software Software Name Purpose MxDC data collection REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing