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Crystal structure of Klebsiella pneumoniae fosfomycin resistance protein (FosAKP) with inhibitor (ANY1) 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 4.6 298 Protein stock:
12mg/ml FosAKP
6mM MnCl2
2.5mM ANY1
100mM KCl
Centrifuge 19,150 x g for 10 min then take 1uL supernatant and combine with 1uL mother liquor (0.02M CaCl2, 0.1M sodium acetate pH 4.6, 30% MPD) in hanging drops.
Crystal Properties Matthews coefficient Solvent content 2.67 53.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.399 α = 90 b = 197.615 β = 90 c = 117.027 γ = 90
Symmetry Space Group C 2 2 21
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 2017-01-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 3.178 39.01 90 0.326 0.371 0.171 0.955 4.3 3.8 21310 47.54
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.18 3.4 91.6 0.968 1.102 0.506 0.577 3.8
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 FREE R-VALUE 5V3D 3.178 37.748 1.34 21263 1105 89.02 0.2229 0.2209 0.2244 0.2621 0.2631 41.8813
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 8.726 f_angle_d 0.492 f_chiral_restr 0.04 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8406 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 248
Software Software Software Name Purpose Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction