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Crystal structure of Yersinia enterocolitica salicylate synthase (Irp9)
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 2.39 48.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.74 α = 90 b = 145.671 β = 107.97 c = 58.807 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 CCD ADSC QUANTUM 4 2005-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 1.488 SRS PX14.1
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 1.85 30 93.9 0.048 0.048 16.1 3.8 77309 72593 2.5 2.5 26.7
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) 1.85 1.89 87.5 0.306 0.306 3.8 5176
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 1.85 28.17 73421 68906 3649 93.85 0.18988 0.18988 0.18717 0.1902 0.24035 0.1879 RANDOM 30.577
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] -0.03 -0.03 0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.796 r_dihedral_angle_4_deg 16.432 r_dihedral_angle_3_deg 13.487 r_dihedral_angle_1_deg 6.411 r_scangle_it 5.29 r_mcangle_it 4.08 r_scbond_it 3.839 r_mcbond_it 3.261 r_angle_refined_deg 1.506 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.796 r_dihedral_angle_4_deg 16.432 r_dihedral_angle_3_deg 13.487 r_dihedral_angle_1_deg 6.411 r_scangle_it 5.29 r_mcangle_it 4.08 r_scbond_it 3.839 r_mcbond_it 3.261 r_angle_refined_deg 1.506 r_nbtor_refined 0.303 r_xyhbond_nbd_refined 0.209 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.179 r_symmetry_hbond_refined 0.114 r_chiral_restr 0.106 r_metal_ion_refined 0.07 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6318 Nucleic Acid Atoms Solvent Atoms 550 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement X-GEN data reduction SCALEPACK data scaling AMoRE phasing