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Crystal structures of Yersinia enterocolitica salicylate synthase (Irp9) in complex with the reaction products salicylate and pyruvate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QDL composite search probe from 1QDL, 1I7Q and 1I1Q experimental model PDB 1I7Q composite search probe from 1QDL, 1I7Q and 1I1Q experimental model PDB 1I1Q composite search probe from 1QDL, 1I7Q and 1I1Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 290 0.2M magnesium acetate tetrahydrate, 0.1M sodium cacodylate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.37 48.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.571 α = 90 b = 145.298 β = 108.39 c = 58.86 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV Rigaku Max Flux mirrors 2005-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.1 30 94 0.049 0.049 20.7 4.8 52602 49446 2.5 2.5 33.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.15 88.7 0.299 0.299 4.7 3453
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT composite search probe from 1QDL, 1I7Q and 1I1Q 2.1 27.37 46901 46901 2513 93.62 0.19091 0.19091 0.18803 0.1904 0.24516 0.1909 RANDOM 33.63
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] -0.07 -0.1 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.635 r_dihedral_angle_4_deg 16.422 r_dihedral_angle_3_deg 14.004 r_dihedral_angle_1_deg 6.61 r_scangle_it 5.39 r_mcangle_it 4.154 r_scbond_it 4.008 r_mcbond_it 3.335 r_angle_refined_deg 1.527 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.635 r_dihedral_angle_4_deg 16.422 r_dihedral_angle_3_deg 14.004 r_dihedral_angle_1_deg 6.61 r_scangle_it 5.39 r_mcangle_it 4.154 r_scbond_it 4.008 r_mcbond_it 3.335 r_angle_refined_deg 1.527 r_nbtor_refined 0.301 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.176 r_xyhbond_nbd_refined 0.165 r_symmetry_hbond_refined 0.161 r_chiral_restr 0.097 r_metal_ion_refined 0.045 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6241 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction SCALEPACK data scaling AMoRE phasing