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Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with cytidine and FOL955, 4-(1H-imidazol)-1-yl)phenol
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 289 27 mg/mL protein in 20% PEG 4000, 100 mM Tris, 200 mM NaCl, 5 mM ZnCl2. Crystals soaked in 25 mM cytidine and FOLMSR in same buffer for 3 weeks., pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.02 39.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.55 α = 90 b = 67.63 β = 95.99 c = 59.77 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+ 2010-08-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54178
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 1.95 20 99.1 0.056 17.91 33803 -3
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 1.95 2 97.5 0.426 2.1
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 1.95 19.83 32038 1712 99.04 0.15425 0.15226 0.1761 0.19102 0.2141 RANDOM 26.989
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 32.397 r_dihedral_angle_4_deg 15.441 r_dihedral_angle_3_deg 12.954 r_dihedral_angle_1_deg 5.692 r_scangle_it 3.057 r_scbond_it 2.116 r_angle_refined_deg 1.548 r_mcangle_it 1.209 r_angle_other_deg 0.949 r_mcbond_it 0.731
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.397 r_dihedral_angle_4_deg 15.441 r_dihedral_angle_3_deg 12.954 r_dihedral_angle_1_deg 5.692 r_scangle_it 3.057 r_scbond_it 2.116 r_angle_refined_deg 1.548 r_mcangle_it 1.209 r_angle_other_deg 0.949 r_mcbond_it 0.731 r_mcbond_other 0.228 r_chiral_restr 0.092 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3402 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms 68
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction