5KGJ

X-ray structure of a glucosamine N-Acetyltransferase from Clostridium acetobutylicum in complex with galactosamine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5KF1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82937-10% PEG-5000, 100 mM HEPPS, 20 mM galactosamine
Crystal Properties
Matthews coefficientSolvent content
2.1743.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.076α = 90
b = 43.84β = 120.81
c = 74.169γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 1352015-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
11.95097.90.0720.07211.64.425686
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9293.60.3022.42.5

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 REPLACEMENTTHROUGHOUT5KF11.95024410127597.90.170.1670.215RANDOM22.83
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]
0.09-0.522.06-0.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.577
r_dihedral_angle_3_deg16.064
r_dihedral_angle_4_deg12.626
r_dihedral_angle_1_deg7.412
r_long_range_B_refined6.769
r_long_range_B_other6.769
r_scangle_other5.257
r_mcangle_it3.552
r_mcangle_other3.551
r_scbond_it3.482
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.577
r_dihedral_angle_3_deg16.064
r_dihedral_angle_4_deg12.626
r_dihedral_angle_1_deg7.412
r_long_range_B_refined6.769
r_long_range_B_other6.769
r_scangle_other5.257
r_mcangle_it3.552
r_mcangle_other3.551
r_scbond_it3.482
r_scbond_other3.481
r_mcbond_it2.422
r_mcbond_other2.419
r_angle_refined_deg1.847
r_angle_other_deg0.859
r_chiral_restr0.278
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms2615
Nucleic Acid Atoms
Solvent Atoms177
Heterogen Atoms114

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing