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Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with diadenosine tetraphosphate (Ap4A) obtained after co-crystallization with ATP
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, 17% (w/v) polyethylene glycol monomethyl ether 5000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.59 52.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.483 α = 90 b = 110.483 β = 90 c = 66.607 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 RIGAKU 2005-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0 SPring-8 BL26B1
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 1.98 50 99.9 0.073 24.41 13.88 32959 45.2
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) 1.98 2.05 100 0.494 2.19 4.9 3248
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 1.98 30 29989 1596 95.94 0.19207 0.19055 0.1928 0.22092 0.2191 RANDOM 25.577
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] 1.61 0.81 1.61 -2.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.497 r_dihedral_angle_4_deg 18.982 r_dihedral_angle_3_deg 13.617 r_dihedral_angle_1_deg 5.695 r_scangle_it 2.35 r_scbond_it 1.425 r_angle_refined_deg 1.177 r_mcangle_it 1.077 r_angle_other_deg 0.89 r_mcbond_it 0.639
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.497 r_dihedral_angle_4_deg 18.982 r_dihedral_angle_3_deg 13.617 r_dihedral_angle_1_deg 5.695 r_scangle_it 2.35 r_scbond_it 1.425 r_angle_refined_deg 1.177 r_mcangle_it 1.077 r_angle_other_deg 0.89 r_mcbond_it 0.639 r_symmetry_vdw_other 0.228 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.194 r_nbd_other 0.189 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.134 r_symmetry_hbond_refined 0.12 r_mcbond_other 0.1 r_nbtor_other 0.082 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2955 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling