7CSI

Aminoglycoside 2'-N-acetyltransferase from Mycolicibacterium smegmatis-Complex with Coenzyme A and Sisomicin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7CRM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2950.2M sodium chloride, 0.1M Tris (pH 8.5), 25% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.4148.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.828α = 90
b = 93.457β = 90
c = 61.395γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2019-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 5C (4A)1PAL/PLS5C (4A)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.895099.80.08929.26.536656
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.891.9296.50.5255.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7CRM1.8942.8834761185399.560.175820.173710.21536RANDOM26.929
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.377
r_dihedral_angle_4_deg18.978
r_dihedral_angle_3_deg13.509
r_long_range_B_refined7.424
r_long_range_B_other7.366
r_dihedral_angle_1_deg7.06
r_scangle_other5.85
r_scbond_it3.8
r_scbond_other3.799
r_mcangle_it3.688
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.377
r_dihedral_angle_4_deg18.978
r_dihedral_angle_3_deg13.509
r_long_range_B_refined7.424
r_long_range_B_other7.366
r_dihedral_angle_1_deg7.06
r_scangle_other5.85
r_scbond_it3.8
r_scbond_other3.799
r_mcangle_it3.688
r_mcangle_other3.687
r_mcbond_it2.567
r_mcbond_other2.567
r_angle_refined_deg1.659
r_angle_other_deg1.412
r_chiral_restr0.08
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms2926
Nucleic Acid Atoms
Solvent Atoms337
Heterogen Atoms158

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling