4KLV

Crystal structure of a GNAT superfamily acetyltransferase PA4794 in complex with 4-methylumbelliferyl phosphate


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
2.448.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.34α = 90
b = 76.486β = 90
c = 39.336γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2010-07-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9794APS19-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
11.339.3799.50.0550.05548.96.14328443284-316.4
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)
11.31.3292.80.5160.5162.84.61978

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 REPLACEMENTTHROUGHOUT2i6c1.339.374096840968216799.50.123950.123950.122420.15198RANDOM19.999
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]
-0.27-0.620.89
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.644
r_dihedral_angle_2_deg35.821
r_dihedral_angle_4_deg17.403
r_rigid_bond_restr14.594
r_sphericity_bonded14.11
r_dihedral_angle_3_deg11.728
r_dihedral_angle_1_deg5.563
r_angle_other_deg3.593
r_angle_refined_deg1.842
r_chiral_restr0.116
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.644
r_dihedral_angle_2_deg35.821
r_dihedral_angle_4_deg17.403
r_rigid_bond_restr14.594
r_sphericity_bonded14.11
r_dihedral_angle_3_deg11.728
r_dihedral_angle_1_deg5.563
r_angle_other_deg3.593
r_angle_refined_deg1.842
r_chiral_restr0.116
r_bond_refined_d0.017
r_gen_planes_other0.017
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1240
Nucleic Acid Atoms
Solvent Atoms239
Heterogen Atoms96

Software

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