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Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with bound CTP and CDP
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 5.9 293 JCSG+ screen condition A5, 20% PEG 3350, 0.2 M Magnesium formate, 34.4 mg/mL Protein, 0.4/0.4 microliter drops, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.03 39.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.703 α = 90 b = 67.548 β = 95.85 c = 60.152 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 Mirrors 2009-06-29 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 2.1 50 99.7 0.06 9.3 3.7 27409
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 2.1 2.14 95.3 0.349 3.1
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 2.1 50 27399 1382 0.202 0.199 0.2038 0.248 0.251 RANDOM 26.94
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] -1.41 1.45 0.98 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.082 r_dihedral_angle_3_deg 14.464 r_dihedral_angle_4_deg 12.472 r_dihedral_angle_1_deg 5.351 r_scangle_it 2.64 r_scbond_it 1.623 r_mcangle_it 1.292 r_angle_refined_deg 1.272 r_angle_other_deg 0.844 r_mcbond_it 0.707
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.082 r_dihedral_angle_3_deg 14.464 r_dihedral_angle_4_deg 12.472 r_dihedral_angle_1_deg 5.351 r_scangle_it 2.64 r_scbond_it 1.623 r_mcangle_it 1.292 r_angle_refined_deg 1.272 r_angle_other_deg 0.844 r_mcbond_it 0.707 r_mcbond_other 0.124 r_chiral_restr 0.07 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 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 3413 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 88
Software Software Software Name Purpose StructureStudio data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling