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Crystal structure of fosfomycin resistance kinase FomA from Streptomyces wedmorensis complexed with MgADP and fosfomycin monophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D40
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 17 % PEG3350, 25 % glycerol, 0.1 M MES, 10 mM ADP, 50 mM MgCl2, 10mM fosfomycin monophosphate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.86 57.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.91 α = 90 b = 87.91 β = 90 c = 79.23 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 2008-01-24 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 1.57 50 95.6 0.035 25 2.4 47552 47552 -3 27.9
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 1.57 1.63 85 0.459 1.5 2.1 4167
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 (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 3D40 1.57 35.14 43681 43681 684 89.21 0.15705 0.15684 0.1673 0.17172 0.1866 RANDOM 32.072
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] 0.58 0.29 0.58 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.693 r_dihedral_angle_4_deg 20.779 r_dihedral_angle_3_deg 14.104 r_dihedral_angle_1_deg 6.106 r_scangle_it 5.16 r_scbond_it 3.244 r_mcangle_it 2.332 r_angle_refined_deg 2.154 r_mcbond_it 1.349 r_angle_other_deg 1.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.693 r_dihedral_angle_4_deg 20.779 r_dihedral_angle_3_deg 14.104 r_dihedral_angle_1_deg 6.106 r_scangle_it 5.16 r_scbond_it 3.244 r_mcangle_it 2.332 r_angle_refined_deg 2.154 r_mcbond_it 1.349 r_angle_other_deg 1.122 r_mcbond_other 0.379 r_chiral_restr 0.134 r_bond_refined_d 0.023 r_gen_planes_refined 0.008 r_bond_other_d 0.003 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 1889 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 40
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling