4OAE

Crystal structure of a GNAT superfamily acetyltransferase PA4794 C29A/C117A/Y128A mutant in complex with chloramphenicol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4KUAPDB ENTRY 4KUA

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
2.4249.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.88α = 90
b = 75.626β = 90
c = 39.482γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2012-11-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.91837APS19-ID

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
11.255099.90.0530.05343.77.34865848658-313.6
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)
11.251.271000.7470.7472.46.32440

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 4KUA1.2545.964615146151245699.920.12210.12210.120370.15476RANDOM19.185
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]
-0.42-0.851.26
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free42.413
r_dihedral_angle_2_deg34.3
r_dihedral_angle_4_deg17.615
r_sphericity_bonded17.322
r_dihedral_angle_3_deg11.088
r_rigid_bond_restr8.645
r_dihedral_angle_1_deg5.667
r_long_range_B_other5.334
r_long_range_B_refined5.331
r_scangle_other4.818
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free42.413
r_dihedral_angle_2_deg34.3
r_dihedral_angle_4_deg17.615
r_sphericity_bonded17.322
r_dihedral_angle_3_deg11.088
r_rigid_bond_restr8.645
r_dihedral_angle_1_deg5.667
r_long_range_B_other5.334
r_long_range_B_refined5.331
r_scangle_other4.818
r_scbond_other4.599
r_scbond_it4.596
r_angle_other_deg3.504
r_mcangle_other1.978
r_mcangle_it1.97
r_angle_refined_deg1.92
r_mcbond_it1.773
r_mcbond_other1.661
r_chiral_restr0.108
r_bond_refined_d0.018
r_gen_planes_other0.015
r_gen_planes_refined0.01
r_bond_other_d
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1239
Nucleic Acid Atoms
Solvent Atoms242
Heterogen Atoms102

Software

Software
Software NamePurpose
HKL-3000data collection
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling