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Crystal structure of human FPPS in complex with three magnesium ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F7M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295.15 1.36 M magnesium sulfate, 15% glycerol, 0.085 M MES
Crystal Properties Matthews coefficient Solvent content 2.77 55.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.34 α = 90 b = 110.34 β = 90 c = 78.52 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 2013-05-29 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 2.1 45.14 99.7 0.04 26.6 8 28729
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 2.1 2.16 99.2 0.709 2.4 7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 2F7M 2.1 45.14 27256 1437 99.67 0.19292 0.19104 0.2057 0.22684 0.238 RANDOM 63.379
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] -4.47 -4.47 8.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.576 r_dihedral_angle_4_deg 19.719 r_dihedral_angle_3_deg 15.048 r_long_range_B_refined 7.731 r_long_range_B_other 7.721 r_dihedral_angle_1_deg 5.873 r_scangle_other 4.947 r_mcangle_it 4.049 r_mcangle_other 4.048 r_scbond_it 3.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.576 r_dihedral_angle_4_deg 19.719 r_dihedral_angle_3_deg 15.048 r_long_range_B_refined 7.731 r_long_range_B_other 7.721 r_dihedral_angle_1_deg 5.873 r_scangle_other 4.947 r_mcangle_it 4.049 r_mcangle_other 4.048 r_scbond_it 3.76 r_scbond_other 3.525 r_mcbond_it 2.876 r_mcbond_other 2.874 r_angle_refined_deg 1.785 r_angle_other_deg 0.892 r_chiral_restr 0.101 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2632 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing