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Crystal structure of Salmonella typhimurium propionate kinase A88G mutant, 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 0.1M Bis-Tris pH 6.5, 30% pentaerythritol ethoxylate, 0.05M ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 2.77 55.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111 α = 90 b = 111 β = 90 c = 66.44 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 2014-02-22 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 2.11 42.59 99 0.1 9.5 5.5 27037
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 2.11 2.23 95.9 0.501 3.2 5.4
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 2.11 42.59 25673 1359 98.77 0.17746 0.17468 0.1842 0.23068 0.2339 RANDOM 37.994
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.105 r_dihedral_angle_4_deg 18.555 r_dihedral_angle_3_deg 14.377 r_long_range_B_refined 7.129 r_long_range_B_other 7.126 r_dihedral_angle_1_deg 6.603 r_scangle_other 5.656 r_mcangle_it 4.276 r_mcangle_other 4.275 r_scbond_it 4.024
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.105 r_dihedral_angle_4_deg 18.555 r_dihedral_angle_3_deg 14.377 r_long_range_B_refined 7.129 r_long_range_B_other 7.126 r_dihedral_angle_1_deg 6.603 r_scangle_other 5.656 r_mcangle_it 4.276 r_mcangle_other 4.275 r_scbond_it 4.024 r_scbond_other 4.022 r_mcbond_it 3.111 r_mcbond_other 3.111 r_angle_refined_deg 1.856 r_angle_other_deg 0.884 r_chiral_restr 0.105 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 2917 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement PHASER phasing SCALA data scaling Coot model building iMOSFLM data extraction