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Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with GTP
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% pentaerythritol ethoxylate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.58 52.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.276 α = 90 b = 110.276 β = 90 c = 66.552 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 2009-05-04 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 2.65 50 99.2 0.097 14.3 11.5 13746
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 2.65 2.74 97.2 0.495 7.7 1338
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 2E1Y 2.65 50 13732 685 99.16 0.2219 0.2193 0.2151 0.274 0.2675 RANDOM 45.5008
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] 1.91 0.95 1.91 -2.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.137 r_dihedral_angle_4_deg 15.098 r_dihedral_angle_3_deg 14.783 r_dihedral_angle_1_deg 4.587 r_angle_refined_deg 0.917 r_scangle_it 0.832 r_mcangle_it 0.529 r_scbond_it 0.458 r_mcbond_it 0.289 r_chiral_restr 0.058
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.137 r_dihedral_angle_4_deg 15.098 r_dihedral_angle_3_deg 14.783 r_dihedral_angle_1_deg 4.587 r_angle_refined_deg 0.917 r_scangle_it 0.832 r_mcangle_it 0.529 r_scbond_it 0.458 r_mcbond_it 0.289 r_chiral_restr 0.058 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2933 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 40
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