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Crystal structure of phosphopantetheine adenylyltransferase from Burkholderia pseudomallei bound to dephospho-coenzyme A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B6T 1B6T molecule A, protein only
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 Hampton Crystal Screen condition c8, 2.0 M ammonium sulfate, 5.5 mg/mL protein with expression tag removed, crystal tracking ID 203611c8, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.67 53.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.161 α = 90 b = 134.161 β = 90 c = 134.161 γ = 90
Symmetry Space Group I 4 3 2
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+ 2009-08-04 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 2.05 50 99 0.087 44.5 23.2 13128
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 2.18 98.1 0.519 6.57 22.4 1181
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 1B6T molecule A, protein only 2.1 28.6 12286 620 99.4 0.2016 0.1995 0.2028 0.2419 0.2196 RANDOM 29.9984
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.607 r_dihedral_angle_4_deg 17.106 r_dihedral_angle_3_deg 14.504 r_dihedral_angle_1_deg 5.26 r_scangle_it 4.257 r_scbond_it 2.584 r_mcangle_it 1.549 r_angle_refined_deg 1.463 r_mcbond_it 0.854 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.607 r_dihedral_angle_4_deg 17.106 r_dihedral_angle_3_deg 14.504 r_dihedral_angle_1_deg 5.26 r_scangle_it 4.257 r_scbond_it 2.584 r_mcangle_it 1.549 r_angle_refined_deg 1.463 r_mcbond_it 0.854 r_chiral_restr 0.095 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1227 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 66
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection HKL-2000 data reduction HKL-2000 data scaling