2QIR

Crystal structure of aminoglycoside acetyltransferase AAC(6')-Ib in complex whith coenzyme A and kanamycin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PRBpdb entry 2prb

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5291K2HPO4 1.5 M, NaH2PO4 0.06M, Guanidine 0.1M, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.7355.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.404α = 90
b = 57.404β = 90
c = 145.57γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDADSC QUANTUM 2102007-05-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.934ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.453.4021000.0810.0818.313.410187101873
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.531000.2120.2123.411.51427

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 2prb2.445.083101871012549099.980.1920.1940.1920.235RANDOM15.601
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]
-0.01-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.254
r_dihedral_angle_4_deg14.672
r_dihedral_angle_3_deg14.086
r_dihedral_angle_1_deg6.411
r_scangle_it2.842
r_scbond_it1.704
r_angle_refined_deg1.349
r_mcangle_it1.202
r_mcbond_it0.75
r_symmetry_hbond_refined0.385
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.254
r_dihedral_angle_4_deg14.672
r_dihedral_angle_3_deg14.086
r_dihedral_angle_1_deg6.411
r_scangle_it2.842
r_scbond_it1.704
r_angle_refined_deg1.349
r_mcangle_it1.202
r_mcbond_it0.75
r_symmetry_hbond_refined0.385
r_nbtor_refined0.3
r_nbd_refined0.196
r_symmetry_vdw_refined0.161
r_xyhbond_nbd_refined0.144
r_chiral_restr0.088
r_bond_refined_d0.011
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1356
Nucleic Acid Atoms
Solvent Atoms78
Heterogen Atoms81

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction