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Crystal structure of fosfomycin resistance kinase FomA from Streptomyces wedmorensis complexed with MgATP
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 5.5 298 17% PEG3350, 15% glycerol, 0.1M MES, 10mM ATP, 10 mM MgCl2, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.76 55.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.876 α = 90 b = 85.876 β = 90 c = 80.152 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 2007-04-16 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 1.87 40 93.4 0.036 32 2.9 26774 26774 -3 33.2
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 1.87 1.94 96.9 0.454 1.9 2.4 2724
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 1.87 23.01 24958 24958 403 88.56 0.18527 0.18494 0.1909 0.20541 0.2302 RANDOM 39.874
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] 0.4 0.2 0.4 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.984 r_dihedral_angle_4_deg 16.864 r_dihedral_angle_3_deg 15.424 r_dihedral_angle_1_deg 6.844 r_scangle_it 3.603 r_scbond_it 2.469 r_mcangle_it 1.915 r_angle_refined_deg 1.763 r_mcbond_it 1.64 r_angle_other_deg 1.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.984 r_dihedral_angle_4_deg 16.864 r_dihedral_angle_3_deg 15.424 r_dihedral_angle_1_deg 6.844 r_scangle_it 3.603 r_scbond_it 2.469 r_mcangle_it 1.915 r_angle_refined_deg 1.763 r_mcbond_it 1.64 r_angle_other_deg 1.005 r_symmetry_vdw_refined 0.401 r_symmetry_vdw_other 0.327 r_mcbond_other 0.285 r_symmetry_hbond_refined 0.244 r_nbd_refined 0.229 r_nbd_other 0.209 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.154 r_xyhbond_nbd_other 0.145 r_chiral_restr 0.1 r_nbtor_other 0.091 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1865 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 38
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling