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Crystal structure of Salmonella typhimurium propionate kinase in complex with AMPPNP and propionate
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 6.5 293.15 0.1 M Bis-Tris pH 6.5, polyethylene glycol 2000
Crystal Properties Matthews coefficient Solvent content 2.8 56.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.61 α = 90 b = 111.61 β = 90 c = 66.65 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 CCD MARMOSAIC 225 mm CCD 2014-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.976 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 32.22 99 0.071 17 7.4 32233 31.469
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 2.11 98.5 0.507 4 7.3
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 32.22 30589 1634 98.77 0.18227 0.17995 0.1895 0.22615 0.2321 RANDOM 34.912
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.667 r_dihedral_angle_4_deg 22.41 r_dihedral_angle_3_deg 14.613 r_long_range_B_refined 7.424 r_long_range_B_other 7.423 r_dihedral_angle_1_deg 6.677 r_scangle_other 6.006 r_mcangle_it 4.533 r_mcangle_other 4.533 r_scbond_it 4.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.667 r_dihedral_angle_4_deg 22.41 r_dihedral_angle_3_deg 14.613 r_long_range_B_refined 7.424 r_long_range_B_other 7.423 r_dihedral_angle_1_deg 6.677 r_scangle_other 6.006 r_mcangle_it 4.533 r_mcangle_other 4.533 r_scbond_it 4.129 r_scbond_other 4.128 r_mcbond_it 3.375 r_mcbond_other 3.368 r_angle_refined_deg 1.953 r_angle_other_deg 0.909 r_chiral_restr 0.116 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2923 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PHASER phasing Coot model building iMOSFLM data reduction