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Crystal structure of human FPPS in complex with one magnesium ion
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, SITTING DROP 6.5 295.15 1.36 M magnesium sulfate, 15% glycerol, 0.085 M MES
Crystal Properties Matthews coefficient Solvent content 2.74 55.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.77 α = 90 b = 110.77 β = 90 c = 76.97 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 2014-02-25 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 2.3 54.9 99.8 0.07 17.3 9.6 21801
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 2.3 2.36 99.5 1.035 2.2 9.7
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 2.3 54.9 20628 1126 99.75 0.19453 0.1924 0.2027 0.23248 0.2335 RANDOM 69.283
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] -3.91 -3.91 7.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.35 r_dihedral_angle_4_deg 20.522 r_dihedral_angle_3_deg 15.519 r_long_range_B_refined 6.809 r_long_range_B_other 6.792 r_dihedral_angle_1_deg 6.057 r_scangle_other 5.073 r_mcangle_it 4.228 r_mcangle_other 4.227 r_scbond_it 3.476
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.35 r_dihedral_angle_4_deg 20.522 r_dihedral_angle_3_deg 15.519 r_long_range_B_refined 6.809 r_long_range_B_other 6.792 r_dihedral_angle_1_deg 6.057 r_scangle_other 5.073 r_mcangle_it 4.228 r_mcangle_other 4.227 r_scbond_it 3.476 r_scbond_other 3.455 r_mcbond_other 2.906 r_mcbond_it 2.905 r_angle_refined_deg 1.627 r_angle_other_deg 0.852 r_chiral_restr 0.09 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 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 2638 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing