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Crystal structure of propionate kinase (TdcD) from Salmonella typhimurium
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 Microbatch method 6.5 293 0.1 Bis-Tris pH 6.5, 30% (v/v) pentaerythritol ethoxylate (15/4 EO/OH), Microbatch method, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.61 52.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.811 α = 90 b = 110.811 β = 90 c = 66.533 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 2005-11-29 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 2.6 30 98.3 0.101 9.7 33.56 14818 57.3
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) 2.6 2.69 84.3 0.45 2.2 1235
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 2.6 30 13415 706 95.52 0.2022 0.19966 0.2012 0.25311 0.2507 RANDOM 34.052
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] 2.1 1.05 2.1 -3.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.526 r_dihedral_angle_4_deg 19.877 r_dihedral_angle_3_deg 13.691 r_dihedral_angle_1_deg 5.554 r_scangle_it 1.199 r_angle_refined_deg 0.932 r_angle_other_deg 0.809 r_mcangle_it 0.697 r_scbond_it 0.685 r_mcbond_it 0.387
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.526 r_dihedral_angle_4_deg 19.877 r_dihedral_angle_3_deg 13.691 r_dihedral_angle_1_deg 5.554 r_scangle_it 1.199 r_angle_refined_deg 0.932 r_angle_other_deg 0.809 r_mcangle_it 0.697 r_scbond_it 0.685 r_mcbond_it 0.387 r_nbd_refined 0.198 r_symmetry_vdw_other 0.19 r_nbd_other 0.178 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.142 r_symmetry_hbond_refined 0.116 r_symmetry_vdw_refined 0.111 r_nbtor_other 0.081 r_chiral_restr 0.054 r_mcbond_other 0.041 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2944 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling