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Crystal structure of human FPPS in complex with magnesium and JDS05120
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 5.9 295 20% PEG 3350, 0.2M magnesium formate, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.37 48.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.51 α = 90 b = 110.51 β = 90 c = 66.97 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 1.85 50.85 99.1 0.042 29.54 9.6 35614 35614 24.99
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 1.85 1.9 99.3 0.437 4.98 9.7 2598
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 4DEM 1.85 50.85 33802 33802 1781 99.19 0.16622 0.16622 0.16464 0.1716 0.19639 0.2025 RANDOM 37.23
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] -2.53 -2.53 5.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.424 r_dihedral_angle_4_deg 21.613 r_dihedral_angle_3_deg 14.818 r_long_range_B_refined 6.305 r_long_range_B_other 6.236 r_dihedral_angle_1_deg 5.256 r_scangle_other 3.894 r_scbond_it 2.593 r_scbond_other 2.592 r_mcangle_it 2.266
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.424 r_dihedral_angle_4_deg 21.613 r_dihedral_angle_3_deg 14.818 r_long_range_B_refined 6.305 r_long_range_B_other 6.236 r_dihedral_angle_1_deg 5.256 r_scangle_other 3.894 r_scbond_it 2.593 r_scbond_other 2.592 r_mcangle_it 2.266 r_mcangle_other 2.266 r_angle_refined_deg 1.857 r_mcbond_it 1.675 r_mcbond_other 1.671 r_angle_other_deg 0.984 r_chiral_restr 0.132 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2748 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 29
Software Software Software Name Purpose MxDC data collection REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing