4EAB

X-ray crystal structure of the H141A mutant of GDP-perosamine N-acetyl transferase 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
2.957.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.968α = 90
b = 114.968β = 90
c = 114.968γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135montel2010-05-18MSINGLE 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
11.355097.250.0530.05316.46.55372853728
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)
11.351.4493.40.3910.3912.138988

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 4EA71.35505372853728273097.250.1880.1880.1870.204RANDOM16.633
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_deg34.511
r_dihedral_angle_4_deg26.782
r_dihedral_angle_3_deg14.306
r_scangle_it7.157
r_dihedral_angle_1_deg6.969
r_scbond_it4.674
r_mcangle_it2.773
r_angle_refined_deg2.1
r_mcbond_it1.75
r_chiral_restr0.162
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.511
r_dihedral_angle_4_deg26.782
r_dihedral_angle_3_deg14.306
r_scangle_it7.157
r_dihedral_angle_1_deg6.969
r_scbond_it4.674
r_mcangle_it2.773
r_angle_refined_deg2.1
r_mcbond_it1.75
r_chiral_restr0.162
r_bond_refined_d0.012
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1460
Nucleic Acid Atoms
Solvent Atoms229
Heterogen Atoms88

Software

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