4L89

Crystal structure of a GNAT superfamily acetyltransferase PA4794 in complex with covalently bound CoA


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52891.5M ammonium sulfate, 0.1M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4850.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.346α = 90
b = 76.673β = 90
c = 40.636γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rmirrors2009-06-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97918APS19-BM

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
11.65099.40.0440.04435.84.72428324283-323.2
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)
11.61.6399.50.5520.55224.71198

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 REPLACEMENTTHROUGHOUT2i6c1.628.692296522965123899.450.159480.159480.157570.19639RANDOM27.71
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]
0.48-1.491.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.339
r_dihedral_angle_4_deg14.338
r_dihedral_angle_3_deg12.02
r_dihedral_angle_1_deg5.855
r_angle_refined_deg1.99
r_angle_other_deg0.905
r_chiral_restr0.119
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.339
r_dihedral_angle_4_deg14.338
r_dihedral_angle_3_deg12.02
r_dihedral_angle_1_deg5.855
r_angle_refined_deg1.99
r_angle_other_deg0.905
r_chiral_restr0.119
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.006
r_gen_planes_other0.002
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 Atoms1226
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms86

Software

Software
Software NamePurpose
HKL-3000data collection
HKL-3000phasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling