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Substrate-bound crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia pseudomallei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TMQ PDB ENTRY 3tmq
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 EBS internal tracking number 227318B6, from a focus screen based on PACT F12.
0.2 M malonate, 0.1 M Bis-Tris propane pH 6.5, 20% PEG3350. BupsA.00102.a.A1 PS00621 at 30.3
mg/mL, 10 mM D-arabinose-5-phosphate, 10 mM phosphoenolpyruvate, vapor diffusion, sitting drop, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.32 51.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.84 α = 90 b = 146.24 β = 90 c = 178.94 γ = 90
Symmetry Space Group P 21 21 21
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+ 2011-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.541780
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 97.3 0.08 19.54 5.6 71084 -3 27.104
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 2.15 94.2 0.376 4.4 4.8
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 MR THROUGHOUT PDB ENTRY 3tmq 2.1 50 71015 3581 97.34 0.168 0.167 0.1695 0.192 0.1962 RANDOM 24.112
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] 0.77 -1.79 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.598 r_dihedral_angle_4_deg 18.461 r_dihedral_angle_3_deg 12.189 r_dihedral_angle_1_deg 6.072 r_angle_refined_deg 1.593 r_angle_other_deg 1.233 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.598 r_dihedral_angle_4_deg 18.461 r_dihedral_angle_3_deg 12.189 r_dihedral_angle_1_deg 6.072 r_angle_refined_deg 1.593 r_angle_other_deg 1.233 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8444 Nucleic Acid Atoms Solvent Atoms 696 Heterogen Atoms 204
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction