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Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with Adenosine Tetraphosphate (AP4)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E1Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.1M Bis-Tris pH 6.5, 30% hexanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.59 52.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.369 α = 90 b = 110.369 β = 90 c = 66.675 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 2009-01-15 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 3 50 98.7 0.139 11.4 7.2 9557
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 3 3.11 90.1 0.562 4.1 852
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2E1Y 3 50 9554 462 98.66 0.2248 0.2222 0.2772 0.2947 RANDOM 49.9779
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] 2.55 1.28 2.55 -3.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.842 r_dihedral_angle_3_deg 14.646 r_dihedral_angle_4_deg 14.511 r_dihedral_angle_1_deg 4.546 r_angle_refined_deg 0.935 r_scangle_it 0.618 r_mcangle_it 0.441 r_scbond_it 0.34 r_mcbond_it 0.241 r_chiral_restr 0.059
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.842 r_dihedral_angle_3_deg 14.646 r_dihedral_angle_4_deg 14.511 r_dihedral_angle_1_deg 4.546 r_angle_refined_deg 0.935 r_scangle_it 0.618 r_mcangle_it 0.441 r_scbond_it 0.34 r_mcbond_it 0.241 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2932 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 43
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection HKL-2000 data reduction