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Linkage between the Bacterial Acid Stress and Stringent Responses: The Structure of the Inducible Lysine Decarboxylase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N75 PDB ENTRY 3N75
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 285 0.1 M Tris, 0.1 M ammonium bromide, 25-35% PEG1000, 0-10% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 4.18 70.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 270.29 α = 90 b = 181.29 β = 125.06 c = 169.93 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 MAR CCD 130 mm 2009-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 CLSI 08ID-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 4.1 140.227 77.4 0.219 0.219 6.2 2.7 52673 40852
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) 4.1 4.32 79.3 0.421 0.421 1.7 2.6
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3N75 4.1 68 38774 2077 77.58 0.27771 0.27629 0.2777 0.30432 0.3046 RANDOM 100.395
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] 3.45 -2.94 -0.01 -6.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.809 r_dihedral_angle_3_deg 13.396 r_dihedral_angle_4_deg 8.446 r_dihedral_angle_1_deg 3.429 r_angle_refined_deg 0.766 r_nbtor_refined 0.293 r_mcangle_it 0.191 r_nbd_refined 0.152 r_scangle_it 0.131 r_symmetry_vdw_refined 0.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.809 r_dihedral_angle_3_deg 13.396 r_dihedral_angle_4_deg 8.446 r_dihedral_angle_1_deg 3.429 r_angle_refined_deg 0.766 r_nbtor_refined 0.293 r_mcangle_it 0.191 r_nbd_refined 0.152 r_scangle_it 0.131 r_symmetry_vdw_refined 0.126 r_symmetry_hbond_refined 0.118 r_mcbond_it 0.107 r_xyhbond_nbd_refined 0.096 r_scbond_it 0.069 r_chiral_restr 0.046 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28485 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MxDC data collection MOSFLM data reduction SCALA data scaling REFMAC phasing