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E. faecium MurAA in complex with fosfomycin and UNAG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3R38
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 2.5mM UNAG and 2.5mM fosfomycin in the buffer containing 0.22 M Potassium sodium tartrate tetrahydrate, 26% w/v Polyethylene glycol 3,350, pH 7.4
Crystal Properties Matthews coefficient Solvent content 3.02 59.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.03 α = 115.06 b = 96.81 β = 99.15 c = 96.821 γ = 103.88
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 300 mm CCD 2018-08-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.65 46.99 97.27 0.101 0.1167 0.995 9.09 4 257217 16.56
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.709 95.68 0.8275 0.956 0.635 1.94 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3R38 1.65 47.82 244512 12707 97.28 0.11788 0.11593 0.15752 0.181 RANDOM 18.24
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] 0.79 -0.09 0.1 -0.02 -0.79 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.13 r_dihedral_angle_4_deg 17.865 r_dihedral_angle_3_deg 11.861 r_dihedral_angle_1_deg 6.146 r_long_range_B_refined 4.419 r_long_range_B_other 4.06 r_rigid_bond_restr 3.77 r_scangle_other 3.546 r_scbond_it 2.89 r_scbond_other 2.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.13 r_dihedral_angle_4_deg 17.865 r_dihedral_angle_3_deg 11.861 r_dihedral_angle_1_deg 6.146 r_long_range_B_refined 4.419 r_long_range_B_other 4.06 r_rigid_bond_restr 3.77 r_scangle_other 3.546 r_scbond_it 2.89 r_scbond_other 2.89 r_mcangle_other 2.637 r_mcangle_it 2.636 r_mcbond_it 2.018 r_mcbond_other 2.014 r_angle_refined_deg 1.705 r_angle_other_deg 1.513 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12721 Nucleic Acid Atoms Solvent Atoms 1596 Heterogen Atoms 205
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing