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High resolution crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphatase synthase from Burkholderia pseudomallei
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 289 PACT screen condition c8, 0.1 M Tris HCL, 20% PEG 4000, 0.2 M NaCl, 34.4. mg/mL protein, 0.4 uL/0.4 uL drops, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.08 40.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.887 α = 90 b = 69.042 β = 130.15 c = 116.581 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 2008-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97934 APS 23-ID-D
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 1.2 50 93.3 0.081 15.8 4 271861
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 1.2 1.29 0.52 2.2 3.3 24496
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 MOLECULAR REPLACEMENT THROUGHOUT 1.2 50 271861 13745 91.16 0.186 0.185 0.1857 0.209 0.2079 RANDOM 20.638
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] -1.75 -0.97 1.94 -1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.309 r_dihedral_angle_3_deg 14.946 r_dihedral_angle_4_deg 13.608 r_sphericity_free 10.168 r_sphericity_bonded 6.366 r_dihedral_angle_1_deg 5.739 r_scangle_it 4.946 r_scbond_it 3.459 r_mcangle_it 2.628 r_mcbond_it 1.776
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.309 r_dihedral_angle_3_deg 14.946 r_dihedral_angle_4_deg 13.608 r_sphericity_free 10.168 r_sphericity_bonded 6.366 r_dihedral_angle_1_deg 5.739 r_scangle_it 4.946 r_scbond_it 3.459 r_mcangle_it 2.628 r_mcbond_it 1.776 r_rigid_bond_restr 1.692 r_angle_refined_deg 1.663 r_angle_other_deg 1.019 r_mcbond_other 0.991 r_chiral_restr 0.11 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6705 Nucleic Acid Atoms Solvent Atoms 504 Heterogen Atoms 6
Software Software Software Name Purpose MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling