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Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with diadenosine tetraphosphate (Ap4A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X3M PDB entry 1X3M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1M Bis-Tris pH 6.5, 45% (v/v) pentaerythritol ethoxylate (15/4 EO/OH), 100mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 52.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.56 α = 90 b = 110.56 β = 90 c = 66.612 γ = 120
Symmetry Space Group P 31 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 IMAGE PLATE MAR scanner 345 mm plate Osmic mirror 2006-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.4 30 99.2 0.074 22.1 31.48 18755 58.02
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) 2.4 2.49 95.2 0.413 3.05 1775
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 FOURIER SYNTHESIS THROUGHOUT PDB entry 1X3M 2.4 30 17574 945 99.28 0.20194 0.19943 0.1997 0.25193 0.253 RANDOM 38.022
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] 2.98 1.49 2.98 -4.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.522 r_dihedral_angle_4_deg 15.339 r_dihedral_angle_3_deg 14.006 r_dihedral_angle_1_deg 5.859 r_scangle_it 1.613 r_angle_refined_deg 1.145 r_scbond_it 1.07 r_angle_other_deg 0.88 r_mcangle_it 0.781 r_mcbond_it 0.705
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.522 r_dihedral_angle_4_deg 15.339 r_dihedral_angle_3_deg 14.006 r_dihedral_angle_1_deg 5.859 r_scangle_it 1.613 r_angle_refined_deg 1.145 r_scbond_it 1.07 r_angle_other_deg 0.88 r_mcangle_it 0.781 r_mcbond_it 0.705 r_symmetry_vdw_other 0.223 r_nbd_refined 0.192 r_nbd_other 0.185 r_nbtor_refined 0.167 r_symmetry_vdw_refined 0.143 r_xyhbond_nbd_refined 0.136 r_symmetry_hbond_refined 0.125 r_nbtor_other 0.084 r_mcbond_other 0.075 r_xyhbond_nbd_other 0.067 r_chiral_restr 0.063 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2938 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling