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Crystal structure of an Antibiotic_NAT family aminoglycoside acetyltransferase HMB0038 from an uncultured soil metagenomic sample in complex with coenzyme A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NYG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 11 298 2 M ammonium sulfate, 0.5 M Capso pH 11, 10mM sisomycin, 5mM coenzyme A
Crystal Properties Matthews coefficient Solvent content 3.61 65.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.016 α = 90 b = 159.501 β = 94.74 c = 146.225 γ = 90
Symmetry Space Group C 1 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 MARMOSAIC 300 mm CCD 2015-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.75 25 96.7 0.074 17.76 4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.8 90.4 0.44 3.19 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 2NYG 2.752 24.973 1.34 60061 2021 95.13 0.2048 0.2038 0.2076 0.2331 0.2358 Random selection
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.967 f_angle_d 1.827 f_chiral_restr 0.066 f_bond_d 0.014 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12016 Nucleic Acid Atoms Solvent Atoms 340 Heterogen Atoms 393
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling BALBES phasing PHENIX model building Coot model building