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Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia cenocepacia
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3T4C PDB ENTRY 3T4C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 EBS internal tracking number 224146E2. JCSG E2.
2000 mM Ammonium sulfate, cacodylate 6.5, 200 mM NaCl. BuceA.00102.a.A1 PS01142 at 74
mg/mL, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.16 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.38 α = 90 b = 149.01 β = 90 c = 151.07 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 MARMOSAIC 300 mm CCD 2011-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03320 APS 23-ID-B
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 1.9 43.26 99.6 0.079 11.54 4 85003 -3 28.944
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 1.9 1.95 99.7 0.564 2.4 4.1
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 3T4C 1.9 43.26 85003 4254 99.59 0.189 0.187 0.1957 0.225 0.2326 RANDOM 31.089
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] 2.43 -1.25 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.667 r_dihedral_angle_4_deg 21.633 r_dihedral_angle_3_deg 13.041 r_dihedral_angle_1_deg 5.369 r_angle_refined_deg 1.462 r_angle_other_deg 0.955 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.667 r_dihedral_angle_4_deg 21.633 r_dihedral_angle_3_deg 13.041 r_dihedral_angle_1_deg 5.369 r_angle_refined_deg 1.462 r_angle_other_deg 0.955 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7855 Nucleic Acid Atoms Solvent Atoms 405 Heterogen Atoms 34
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection XDS data reduction