4KOT

Crystal structure of a GNAT superfamily acetyltransferase PA4794 in complex with Cefotaxime


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2I6C 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52892M ammonium sulfate, 0.1M Bis-Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4549.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.75α = 90
b = 76.296β = 90
c = 39.298γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBeryllium Lenses2013-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
11.555099.70.0390.03943.95.72623826238-323.3
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)
11.551.5898.90.6250.6252.45.61269

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 REPLACEMENTTHROUGHOUT2i6c1.5532.692486924869132799.60.158310.158310.156640.18975RANDOM26.981
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]
1.06-1.090.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.677
r_dihedral_angle_4_deg17.554
r_dihedral_angle_3_deg11.877
r_dihedral_angle_1_deg5.391
r_angle_refined_deg1.992
r_angle_other_deg0.921
r_chiral_restr0.12
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.677
r_dihedral_angle_4_deg17.554
r_dihedral_angle_3_deg11.877
r_dihedral_angle_1_deg5.391
r_angle_refined_deg1.992
r_angle_other_deg0.921
r_chiral_restr0.12
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_bond_other_d0.002
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1239
Nucleic Acid Atoms
Solvent Atoms188
Heterogen Atoms70

Software

Software
Software NamePurpose
HKL-3000phasing
REFMACrefinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling