8E62

STRUCTURE OF Pcryo_0615 from Psychrobacter cryohalolentis, an N-acetyltransferase required to produce Diacetamido-2,3-dideoxy-D-glucuronic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5DEM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6293Protein incubated with: 5 mM CoA and 5 mM UDP-GlcNAc3NA. Precipitant: 16 - 20% PEG-3350, 2% 2-methyl-2,4-pentanediol, and 100 mM MES (pH 6.0)
Crystal Properties
Matthews coefficientSolvent content
2.4148.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.113α = 90
b = 79.768β = 114.28
c = 96.616γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702019-08-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.9792APS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.85098.10.07930.84.3102909
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8396.20.2265.33.6

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5dem1.848.1597882502798.040.1680.16590.2081RANDOM22.1
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.66
r_dihedral_angle_4_deg23.071
r_dihedral_angle_3_deg15.932
r_dihedral_angle_1_deg7.35
r_angle_refined_deg1.557
r_angle_other_deg1.325
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.66
r_dihedral_angle_4_deg23.071
r_dihedral_angle_3_deg15.932
r_dihedral_angle_1_deg7.35
r_angle_refined_deg1.557
r_angle_other_deg1.325
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8172
Nucleic Acid Atoms
Solvent Atoms631
Heterogen Atoms410

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing