☰ Navigation Tabs
Aminoglycoside 2'-N-acetyltransferase from Mycolicibacterium smegmatis-Complex with Coenzyme A and Sisomicin
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 sodium chloride, 0.1M Tris (pH 8.5), 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.41 48.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.828 α = 90 b = 93.457 β = 90 c = 61.395 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2019-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1 PAL/PLS 5C (4A)
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 1.89 50 99.8 0.089 29.2 6.5 36656
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 1.89 1.92 96.5 0.525 5.3
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 1.89 42.88 34761 1853 99.56 0.17582 0.17371 0.1826 0.21536 0.2213 RANDOM 26.929
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.377 r_dihedral_angle_4_deg 18.978 r_dihedral_angle_3_deg 13.509 r_long_range_B_refined 7.424 r_long_range_B_other 7.366 r_dihedral_angle_1_deg 7.06 r_scangle_other 5.85 r_scbond_it 3.8 r_scbond_other 3.799 r_mcangle_it 3.688
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.377 r_dihedral_angle_4_deg 18.978 r_dihedral_angle_3_deg 13.509 r_long_range_B_refined 7.424 r_long_range_B_other 7.366 r_dihedral_angle_1_deg 7.06 r_scangle_other 5.85 r_scbond_it 3.8 r_scbond_other 3.799 r_mcangle_it 3.688 r_mcangle_other 3.687 r_mcbond_it 2.567 r_mcbond_other 2.567 r_angle_refined_deg 1.659 r_angle_other_deg 1.412 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 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 2926 Nucleic Acid Atoms Solvent Atoms 337 Heterogen Atoms 158
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling