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Crystal structure of fosfomycin resistance kinase FomA from Streptomyces wedmorensis complexed with MgAMPPNP and fosfomycin
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 7 295 11% PEG 3350, 0.1 M tri-ammonium citrate, 0.1 M MES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.71 54.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.656 α = 90 b = 85.656 β = 90 c = 78.979 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 2007-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CAMD BEAMLINE GCPCC 1.38074 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 2.2 50 99.6 0.071 19.2 4.1 17293 17293 -3 46.3
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 2.2 2.28 97.9 0.557 1.8 3.4 1664
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 PDB ENTRY 3D40 2.2 29.04 15587 15587 215 90.97 0.193 0.193 0.1919 0.252 0.2539 RANDOM 43.194
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] 2.11 1.06 2.11 -3.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.522 r_dihedral_angle_4_deg 21.808 r_dihedral_angle_3_deg 17.794 r_dihedral_angle_1_deg 7.079 r_scangle_it 3.092 r_scbond_it 1.854 r_angle_refined_deg 1.727 r_mcangle_it 1.233 r_mcbond_it 0.712 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.522 r_dihedral_angle_4_deg 21.808 r_dihedral_angle_3_deg 17.794 r_dihedral_angle_1_deg 7.079 r_scangle_it 3.092 r_scbond_it 1.854 r_angle_refined_deg 1.727 r_mcangle_it 1.233 r_mcbond_it 0.712 r_nbtor_refined 0.309 r_symmetry_hbond_refined 0.239 r_nbd_refined 0.216 r_symmetry_vdw_refined 0.203 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.1 r_metal_ion_refined 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2024 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing