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Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei in complex with 5'-iodo-cytosine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.9 289 20% PEG 3350, 0.2 M magnesium formate, 34.4 mg/mL protein,
5 mM 5'-iodo-cytosine soak for 5 days, crystal tracking ID 205278a4, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.03 39.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.475 α = 90 b = 67.673 β = 96.13 c = 60.025 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+ 2009-09-28 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 1.85 50 98.6 0.078 16.3 3.5 39427
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 1.92 90.8 0.249 2.29 1.9 3606
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 PDB entry 3F0E THROUGHOUT 1.85 27.18 39395 1972 98.34 0.172 0.17 0.1704 0.204 0.206 RANDOM 17.788
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] -1.78 -0.34 1.96 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.126 r_dihedral_angle_4_deg 17.782 r_dihedral_angle_3_deg 12.675 r_dihedral_angle_1_deg 5.3 r_scangle_it 3.356 r_scbond_it 2.109 r_angle_refined_deg 1.414 r_mcangle_it 1.172 r_mcbond_it 0.699 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.126 r_dihedral_angle_4_deg 17.782 r_dihedral_angle_3_deg 12.675 r_dihedral_angle_1_deg 5.3 r_scangle_it 3.356 r_scbond_it 2.109 r_angle_refined_deg 1.414 r_mcangle_it 1.172 r_mcbond_it 0.699 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3338 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 56
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing