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X-ray Crystal Structure of the Escherichia coli Inducible Lysine Decarboxylase LdcI
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ORD PDB ENTRY 1ORD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 285 18-28% (v/v) PEG1000, 0.1 M Sodium Chloride, 0.1 M Tris HCl pH 8.5, 0.005 M Tris[2-carboxyethyl] phosphine, 15% (v/v) glycerol. Once crystals formed, they were soaked in mother liquid that had been saturated with hexatantalum dodecabromide for derivatization., VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 4.22 70.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 271.76 α = 90 b = 181.993 β = 125.41 c = 170.902 γ = 90
Symmetry Space Group C 1 2 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 SBC-3 2006-03-22 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 2006-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 1.254431 APS 19-BM 2 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9002 APS 14-BM-C
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 2 140.3 99.8 0.161 12.6 5.44 454474 454474
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 2 2.1 99.3 0.3266 3.82 3.39 61407
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 (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 1ORD 2 49.89 454474 430750 22770 99.76 0.16886 0.16753 0.1685 0.19392 0.1941 RANDOM 27.734
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] 0.43 -0.84 0.32 -1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.012 r_dihedral_angle_4_deg 15.212 r_dihedral_angle_3_deg 12.802 r_dihedral_angle_1_deg 12.177 r_scangle_it 4.244 r_scbond_it 2.865 r_angle_refined_deg 1.633 r_mcangle_it 1.562 r_mcbond_it 1.364 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.012 r_dihedral_angle_4_deg 15.212 r_dihedral_angle_3_deg 12.802 r_dihedral_angle_1_deg 12.177 r_scangle_it 4.244 r_scbond_it 2.865 r_angle_refined_deg 1.633 r_mcangle_it 1.562 r_mcbond_it 1.364 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.219 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.148 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.113 r_bond_refined_d 0.016 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28485 Nucleic Acid Atoms Solvent Atoms 3292 Heterogen Atoms 293
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling