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Crystal Structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) from Burkholderia thailandensis complexed with CTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YS8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.05 290 ButhA.00168.a.A1.PW33338 at 30.46 mg/ml mixed 1:1 with JCSG+(e11): 10.73% PEG-8000, 80mM Sodium Cacodylate/ HCl, pH=6.04, 160mM Calcium acetate, 20% glycerol. Apo crystals were soaked with 1mM MgCl2, CTP, and D-erythritol-4-phosphate
Crystal Properties Matthews coefficient Solvent content 2.32 47.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.9 α = 90 b = 138.95 β = 101.94 c = 76.92 γ = 90
Symmetry Space Group P 1 21 1
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 MARMOSAIC 300 mm CCD Beryllium Lenses 2015-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 50 99.7 0.081 0.094 13.44 3.8 41718 -3 31.72
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.36 99.6 0.539 0.626 2.84
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 4YS8 2.3 26.932 1.35 41687 1948 99.75 0.2074 0.205 0.2059 0.2571 0.2576 41.7333
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.067 f_angle_d 0.563 f_chiral_restr 0.028 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6652 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 111
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHENIX phasing