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Aminoglycoside 2'-N-acetyltransferase from Mycolicibacterium smegmatis-Complex with Coenzyme A and Paromomycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7CRM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 0.2M calcium acetate hydrate, 0.1M HEPES (pH 7.5), 10% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.43 49.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.374 α = 90 b = 56.374 β = 90 c = 122.866 γ = 120
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 ADSC QUANTUM 270 2019-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97935 PAL/PLS 7A (6B, 6C1)
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 2.05 50 99.9 0.101 31.56 5.6 27416
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 2.05 2.09 100 0.266 5.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 7CRM 2.05 28.2 25966 1413 99.87 0.18564 0.18306 0.1903 0.23323 0.2362 RANDOM 22.873
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.712 r_dihedral_angle_4_deg 15.923 r_dihedral_angle_3_deg 15.385 r_dihedral_angle_1_deg 7.516 r_long_range_B_refined 6.793 r_long_range_B_other 6.741 r_scangle_other 4.482 r_mcangle_it 3.351 r_mcangle_other 3.351 r_scbond_it 2.806
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.712 r_dihedral_angle_4_deg 15.923 r_dihedral_angle_3_deg 15.385 r_dihedral_angle_1_deg 7.516 r_long_range_B_refined 6.793 r_long_range_B_other 6.741 r_scangle_other 4.482 r_mcangle_it 3.351 r_mcangle_other 3.351 r_scbond_it 2.806 r_scbond_other 2.805 r_mcbond_it 2.117 r_mcbond_other 2.117 r_angle_refined_deg 1.643 r_angle_other_deg 1.312 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2912 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 199
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling