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Crystal structure of Klebsiella pneumoniae fosfomycin resistance protein (FosAKP) with inhibitor (ANY2) bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5V3D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 Mother liquor:
20% PEG 3350
0.1M Bis Tris pH 5.5
0.2M NH4SO4
Protein at 11.5 mg/mL was combined with ANY2 at a final concentration of 2.5mM, and MnCl2 at 0.6mM. Sample was centrifuged and supernatant 1uL of supernatant was combined with 1uL of mother liquor. Crystals were improved by streak seeding
Crystal Properties Matthews coefficient Solvent content 2.13 42.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.765 α = 90 b = 68.837 β = 90.46 c = 90.312 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS3 S 6M 2017-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9795 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.85 37.53 95 9.01 3.4 45290
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.916 97 1.76 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5v3d 1.85 37.527 1.35 44417 2280 94.62 0.1859 0.1845 0.1852 0.2118 0.2132 21.6612
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 f_dihedral_angle_d 10.899 f_angle_d 0.638 f_chiral_restr 0.044 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4273 Nucleic Acid Atoms Solvent Atoms 714 Heterogen Atoms 86
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction MOLREP phasing