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Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with CMP
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 6 298 0.1M Bis-Tris pH 6.0, 35% pentaerythritol ethoxylate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.63 53.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.252 α = 90 b = 111.252 β = 90 c = 66.598 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 2008-10-04 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 3 50 98.9 0.124 14.3 10.5 9701
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 94.2 0.583 6.5 910
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 3 50 9700 466 98.92 0.2115 0.2097 0.2075 0.2504 0.2494 RANDOM 51.0122
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] 2.18 1.09 2.18 -3.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.777 r_dihedral_angle_4_deg 16.279 r_dihedral_angle_3_deg 15.539 r_dihedral_angle_1_deg 4.801 r_angle_refined_deg 0.939 r_scangle_it 0.827 r_mcangle_it 0.576 r_scbond_it 0.448 r_mcbond_it 0.315 r_chiral_restr 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.777 r_dihedral_angle_4_deg 16.279 r_dihedral_angle_3_deg 15.539 r_dihedral_angle_1_deg 4.801 r_angle_refined_deg 0.939 r_scangle_it 0.827 r_mcangle_it 0.576 r_scbond_it 0.448 r_mcbond_it 0.315 r_chiral_restr 0.06 r_bond_refined_d 0.006 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2946 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 29
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 HKL-2000 data scaling