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Crystal structure of fosfomycin resistance kinase FomA from Streptomyces wedmorensis complexed with diphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other model of SeMet FomA form based on MAD data
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 2.88 57.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.361 α = 90 b = 88.361 β = 90 c = 79.046 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 2007-03-27 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 1.53 30 97.9 0.04 34.8 5.2 52986 52986 -3 27.7
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) 1.53 1.58 85.3 0.51 2.9 4.6 4585
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT model of SeMet FomA form based on MAD data 1.53 27.49 50201 50201 834 94.29 0.16908 0.16908 0.16864 0.1842 0.19801 0.2101 RANDOM 26.933
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] 0.36 0.18 0.36 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.6 r_dihedral_angle_4_deg 14.671 r_dihedral_angle_3_deg 13.526 r_dihedral_angle_1_deg 5.409 r_scangle_it 4.418 r_scbond_it 2.803 r_mcangle_it 1.917 r_angle_refined_deg 1.738 r_mcbond_it 1.25 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.6 r_dihedral_angle_4_deg 14.671 r_dihedral_angle_3_deg 13.526 r_dihedral_angle_1_deg 5.409 r_scangle_it 4.418 r_scbond_it 2.803 r_mcangle_it 1.917 r_angle_refined_deg 1.738 r_mcbond_it 1.25 r_nbtor_refined 0.318 r_nbd_refined 0.211 r_symmetry_hbond_refined 0.175 r_symmetry_vdw_refined 0.169 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.123 r_bond_refined_d 0.016 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1953 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing