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Crystal Structure of FosB from Enterococcus faecium with Fosfomycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JH2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 20 mg/mL protein in 20mM HEPES pH7.5, 38% PEG MME 550, 150mM Magnesium Chloride
Crystal Properties Matthews coefficient Solvent content 2.32 46.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.874 α = 90 b = 79.874 β = 90 c = 95.639 γ = 90
Symmetry Space Group P 41 21 2
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 RIGAKU 2019-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
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 2 23.8 99.7 0.102 1.74 18.1 21556 30.7
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 2.07 0.745
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 4JH2 2 23.8 20380 1078 99.67 0.2156 0.2135 0.2231 0.2537 0.2637 RANDOM 31.256
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] -0.44 -0.44 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.286 r_dihedral_angle_4_deg 17.412 r_dihedral_angle_3_deg 14.788 r_dihedral_angle_1_deg 7.813 r_angle_refined_deg 1.641 r_angle_other_deg 1.33 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.286 r_dihedral_angle_4_deg 17.412 r_dihedral_angle_3_deg 14.788 r_dihedral_angle_1_deg 7.813 r_angle_refined_deg 1.641 r_angle_other_deg 1.33 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2228 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SCALA data scaling PHASER phasing CrysalisPro data reduction