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Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with cytosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F0E PDB entry 3F0E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.9 289 20% PEG 3350, 0.2 M Mg Formate, 34.4 MG/ML protein, 0.4/0.4 uL drops, Crystal tracking ID 204112a1, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.28 46.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.659 α = 90 b = 68.064 β = 96.29 c = 60.156 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+ 2009-07-28 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 2.3 50 99.9 0.089 12.8 3.2 21121
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 2.38 100 0.41 2.8 3.2 2105
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3F0E 2.3 28.31 21111 1084 99.7 0.187 0.185 0.1832 0.234 0.2348 RANDOM 26.741
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] -1.36 0.14 1.62 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.953 r_dihedral_angle_4_deg 18.757 r_dihedral_angle_3_deg 15.073 r_dihedral_angle_1_deg 5.78 r_scangle_it 3.438 r_scbond_it 2.161 r_mcangle_it 1.473 r_angle_refined_deg 1.442 r_mcbond_it 0.816 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.953 r_dihedral_angle_4_deg 18.757 r_dihedral_angle_3_deg 15.073 r_dihedral_angle_1_deg 5.78 r_scangle_it 3.438 r_scbond_it 2.161 r_mcangle_it 1.473 r_angle_refined_deg 1.442 r_mcbond_it 0.816 r_chiral_restr 0.097 r_bond_refined_d 0.015 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3398 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 29
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