7CS0

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2950.2M calcium acetate hydrate, 0.1M HEPES (pH 7.5), 10% (w/v) PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.4349.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.374α = 90
b = 56.374β = 90
c = 122.866γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702019-11-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 7A (6B, 6C1)0.97935PAL/PLS7A (6B, 6C1)

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
12.055099.90.10131.565.627416
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)
12.052.091000.2665.7

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-VALUE7CRM2.0528.225966141399.870.185640.183060.23323RANDOM22.873
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]
0.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.712
r_dihedral_angle_4_deg15.923
r_dihedral_angle_3_deg15.385
r_dihedral_angle_1_deg7.516
r_long_range_B_refined6.793
r_long_range_B_other6.741
r_scangle_other4.482
r_mcangle_it3.351
r_mcangle_other3.351
r_scbond_it2.806
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.712
r_dihedral_angle_4_deg15.923
r_dihedral_angle_3_deg15.385
r_dihedral_angle_1_deg7.516
r_long_range_B_refined6.793
r_long_range_B_other6.741
r_scangle_other4.482
r_mcangle_it3.351
r_mcangle_other3.351
r_scbond_it2.806
r_scbond_other2.805
r_mcbond_it2.117
r_mcbond_other2.117
r_angle_refined_deg1.643
r_angle_other_deg1.312
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.008
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 Atoms2912
Nucleic Acid Atoms
Solvent Atoms248
Heterogen Atoms199

Software

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