8VR7

crystal structure of the Pcryo_0619 N-acetyltransferase from Psychrobacter cryohalolentis K5 int he presence of acetyl coenzyme A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8VR6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5293Protein incubated with 3 mM acetyl-CoA. Precipitant: 8-12% PEG 8000 and 100 mM homopipes (pH 5)
Crystal Properties
Matthews coefficientSolvent content
2.3948.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.895α = 90
b = 157.818β = 90
c = 66.046γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELBruker PHOTON II2019-11-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEBRUKER D8 QUEST1.5418

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
11.95099.70.08414.311.589307
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)
11.9299.20.42.85.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.929.6984841446699.70.199480.197330.23993RANDOM18.034
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_3_deg15.192
r_dihedral_angle_2_deg11.503
r_dihedral_angle_1_deg6.671
r_long_range_B_refined5.259
r_long_range_B_other5.259
r_scangle_other3.797
r_mcangle_it2.358
r_mcangle_other2.358
r_scbond_it2.338
r_scbond_other2.338
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.192
r_dihedral_angle_2_deg11.503
r_dihedral_angle_1_deg6.671
r_long_range_B_refined5.259
r_long_range_B_other5.259
r_scangle_other3.797
r_mcangle_it2.358
r_mcangle_other2.358
r_scbond_it2.338
r_scbond_other2.338
r_mcbond_it1.471
r_mcbond_other1.469
r_angle_refined_deg1.366
r_angle_other_deg0.449
r_chiral_restr0.06
r_gen_planes_refined0.007
r_bond_refined_d0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8064
Nucleic Acid Atoms
Solvent Atoms672
Heterogen Atoms355

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing