4EAA

X-ray crystal structure of the H141N mutant of perosamine N-acetyltransferase from Caulobacter crescentus in complex with CoA and GDP-perosamine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4EA7PDB ENTRY 4EA7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529825-30% PEG5000 MME, 100 mM HEPES, pH 7.5, 5 mM CoA, 5 mM GDP, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.8957.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.007α = 90
b = 115.007β = 90
c = 115.007γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135montel2010-04-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.54178

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
11.4581.32299.20.0660.06614.59.34456744567
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)
11.451.5597.40.3640.3642.94.38131

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUTPDB ENTRY 4EA71.4540.66141237220096.770.181120.179580.2099RANDOM16.081
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_deg36.301
r_dihedral_angle_4_deg23.749
r_dihedral_angle_3_deg14.28
r_scangle_it7.632
r_dihedral_angle_1_deg6.992
r_scbond_it4.908
r_mcangle_it2.841
r_angle_refined_deg2.105
r_mcbond_it1.868
r_chiral_restr0.174
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.301
r_dihedral_angle_4_deg23.749
r_dihedral_angle_3_deg14.28
r_scangle_it7.632
r_dihedral_angle_1_deg6.992
r_scbond_it4.908
r_mcangle_it2.841
r_angle_refined_deg2.105
r_mcbond_it1.868
r_chiral_restr0.174
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1463
Nucleic Acid Atoms
Solvent Atoms200
Heterogen Atoms88

Software

Software
Software NamePurpose
PROTEUM PLUSdata collection
PHASERphasing
REFMACrefinement
SAINTdata reduction
SADABSdata scaling