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Crystal structure of 2-amino-2-desoxyisochorismate synthase (ADIC) synthase PhzE from Burkholderia lata 383 in complex with benzoate, pyruvate and glutamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3R75 PDB ENTRY 3R75
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.1 276 0.1 M HEPES, 0.2 M Mg-chloride, 22% isopropanol, pre-incubation on ice for 30' with 50 mM Mg-chloride, 20 mM glutamine, 20 mM chorismate, streak-seeding, pH 7.1, vapor diffusion, hanging drop, temperature 276K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.44 49.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 258.166 α = 90 b = 97.792 β = 90 c = 53.988 γ = 90
Symmetry Space Group P 21 21 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 MARMOSAIC 225 mm CCD SI(111) 2009-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.979 SLS X10SA
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 2.6 29.664 99.8 0.06 17.71 43071 -3 47.384
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 2.6 2.7 100 0.357 4.45
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 3R75 2.6 29.66 43043 2227 99.84 0.1665 0.1633 0.1654 0.225 0.2232 RANDOM 52.2518
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] -1.57 -1.42 2.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.861 r_dihedral_angle_4_deg 18.717 r_dihedral_angle_3_deg 16.607 r_dihedral_angle_1_deg 6.301 r_angle_other_deg 2.461 r_angle_refined_deg 1.572 r_chiral_restr 0.083 r_bond_refined_d 0.016 r_bond_other_d 0.007 r_gen_planes_refined 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.861 r_dihedral_angle_4_deg 18.717 r_dihedral_angle_3_deg 16.607 r_dihedral_angle_1_deg 6.301 r_angle_other_deg 2.461 r_angle_refined_deg 1.572 r_chiral_restr 0.083 r_bond_refined_d 0.016 r_bond_other_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9278 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 42
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction