2PRB

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PR8pdb entry 2PR8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72911.5 M K2HPO4 0.06M NaH2PO4 0.1M guanidine-HCl, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.7855.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.62α = 90
b = 57.62β = 90
c = 146.672γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDADSC QUANTUM 4r2007-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-30.9310ESRFID14-3

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
11.853.631000.0590.0598.313.523842238361
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)
1.81.91000.1830.1834.110.53394

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 2PR81.840.762376523761121999.980.2090.210.2090.226RANDOM15.468
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.842
r_dihedral_angle_4_deg12.229
r_dihedral_angle_3_deg10.485
r_dihedral_angle_1_deg4.859
r_scangle_it1.804
r_scbond_it1.044
r_angle_refined_deg1.003
r_mcangle_it0.753
r_mcbond_it0.411
r_nbtor_refined0.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.842
r_dihedral_angle_4_deg12.229
r_dihedral_angle_3_deg10.485
r_dihedral_angle_1_deg4.859
r_scangle_it1.804
r_scbond_it1.044
r_angle_refined_deg1.003
r_mcangle_it0.753
r_mcbond_it0.411
r_nbtor_refined0.295
r_nbd_refined0.176
r_symmetry_vdw_refined0.128
r_xyhbond_nbd_refined0.087
r_symmetry_hbond_refined0.085
r_chiral_restr0.063
r_bond_refined_d0.006
r_gen_planes_refined0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1360
Nucleic Acid Atoms
Solvent Atoms172
Heterogen Atoms48

Software

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