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Crystal structure of fosfomycin resistance kinase FomA from Streptomyces wedmorensis complexed with MgADP and fosfomycin vanadate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D40 pdb entry 3D40
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 17% PEG3350, 25% glycerol, 0.1M MES, 10mM AD, 50mM MgCl2, 10mM fosfomycin, 10mM NaVO3, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.82 56.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.38 α = 90 b = 87.38 β = 90 c = 79 γ = 120
Symmetry Space Group P 32 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 MAR CCD 165 mm mirrors 2008-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CAMD BEAMLINE GCPCC 1.38079 CAMD GCPCC
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 1.85 40 99.3 0.046 31.4 4.9 29919 29919 -3 34.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 99.3 0.705 1.7 4 2931
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 pdb entry 3D40 1.85 27.32 27413 27413 411 92.25 0.16485 0.16485 0.16407 0.21938 0.2501 RANDOM 41.142
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] 0.66 0.33 0.66 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.072 r_dihedral_angle_4_deg 20.291 r_dihedral_angle_3_deg 15.679 r_dihedral_angle_1_deg 7.131 r_scangle_it 4.792 r_scbond_it 3.421 r_angle_refined_deg 2.002 r_mcangle_it 2.002 r_mcbond_it 1.168 r_angle_other_deg 1.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.072 r_dihedral_angle_4_deg 20.291 r_dihedral_angle_3_deg 15.679 r_dihedral_angle_1_deg 7.131 r_scangle_it 4.792 r_scbond_it 3.421 r_angle_refined_deg 2.002 r_mcangle_it 2.002 r_mcbond_it 1.168 r_angle_other_deg 1.131 r_mcbond_other 0.326 r_chiral_restr 0.119 r_bond_refined_d 0.022 r_gen_planes_refined 0.008 r_bond_other_d 0.004 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2064 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 40
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling