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Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with cytosine and FoL fragment 717, imidazo[2,1-b][1,3]thiazol-6-ylmethanol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IKE PDB entry 3ike
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 289 20% PEG 4000, 100 mM Tris, 200 mM NaCl, 5 mM ZnCl2 with 34.4 mg/mL protein
for 3 days. Crystal soaked in 25 mM cytosine and fragment 717 in same buffer for 3 weeks.
VAPOR DIFFUSION, SITTING DROP, temperature 289K, pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.03 39.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.543 α = 90 b = 67.569 β = 96.12 c = 60.03 γ = 90
Symmetry Space Group C 1 2 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 RIGAKU SATURN 944+ 2010-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 1.8 50 88.4 0.081 20.1 1.7 41626
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 1.8 1.83 81.6 0.256 2.52 1.2 3545
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3ike 1.8 25.5 41626 2090 95.95 0.189 0.188 0.217 RANDOM 6.423
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.355 r_dihedral_angle_4_deg 16.935 r_dihedral_angle_3_deg 13.26 r_dihedral_angle_1_deg 5.635 r_scangle_it 2.608 r_angle_refined_deg 1.745 r_scbond_it 1.703 r_angle_other_deg 1.078 r_mcangle_it 1.028 r_mcbond_it 0.591
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.355 r_dihedral_angle_4_deg 16.935 r_dihedral_angle_3_deg 13.26 r_dihedral_angle_1_deg 5.635 r_scangle_it 2.608 r_angle_refined_deg 1.745 r_scbond_it 1.703 r_angle_other_deg 1.078 r_mcangle_it 1.028 r_mcbond_it 0.591 r_mcbond_other 0.136 r_chiral_restr 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3417 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 65
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection