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Salicylate and Pyruvate Bound Structure of the Isochorismate-Pyruvate Lyase K42E Mutant from Pseudomonas aerugionsa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H9D PDB ENTRY 2H9D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.6 298 0.004 M gly-gly, 0.100 M sodium acetate, 12% glycerol, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.74 29.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.144 α = 90 b = 57.313 β = 90 c = 60.334 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 325 mm CCD Rh coated flat mirror, toroidal focusing mirror 2009-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 1.0000 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.79 25.89 97.2 0.098 5.7 3.5 15734 13690
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.84 97.9 0.375 2 3.3 2186
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2H9D 1.79 25.89 15294 13690 1532 97.34 0.21357 0.21357 0.20793 0.26403 0.2989 RANDOM 20.854
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.415 r_dihedral_angle_4_deg 16.521 r_dihedral_angle_3_deg 14.738 r_scangle_it 5.526 r_dihedral_angle_1_deg 5.158 r_scbond_it 3.446 r_mcangle_it 2.055 r_angle_refined_deg 1.874 r_mcbond_it 1.238 r_chiral_restr 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.415 r_dihedral_angle_4_deg 16.521 r_dihedral_angle_3_deg 14.738 r_scangle_it 5.526 r_dihedral_angle_1_deg 5.158 r_scbond_it 3.446 r_mcangle_it 2.055 r_angle_refined_deg 1.874 r_mcbond_it 1.238 r_chiral_restr 0.14 r_bond_refined_d 0.022 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1519 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 32
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling