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Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E1Y PDB ENTRY 2E1Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 0.1M Bis-Tris pH 6.0, 30% hexanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.64 53.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.419 α = 90 b = 111.419 β = 90 c = 66.732 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 Mirror 2009-01-13 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 2.8 50 99.5 0.118 11.8 6.2 12025
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 2.8 2.9 95.9 0.585 5 1128
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 2E1Y 2.8 50 12025 575 99.45 0.2336 0.2312 0.2259 0.2824 0.2721 RANDOM 46.9403
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] 1.8 0.9 1.8 -2.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.758 r_dihedral_angle_4_deg 16.009 r_dihedral_angle_3_deg 14.01 r_dihedral_angle_1_deg 4.348 r_angle_refined_deg 0.893 r_scangle_it 0.494 r_mcangle_it 0.424 r_scbond_it 0.269 r_mcbond_it 0.233 r_chiral_restr 0.054
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.758 r_dihedral_angle_4_deg 16.009 r_dihedral_angle_3_deg 14.01 r_dihedral_angle_1_deg 4.348 r_angle_refined_deg 0.893 r_scangle_it 0.494 r_mcangle_it 0.424 r_scbond_it 0.269 r_mcbond_it 0.233 r_chiral_restr 0.054 r_bond_refined_d 0.005 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2922 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 27
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection PHASER phasing