5KGP

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72937-11% PEG-8000, 100 mM HEPES, 20 mM chitosan
Crystal Properties
Matthews coefficientSolvent content
2.4449.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.147α = 90
b = 65.776β = 106.95
c = 90.803γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 1352015-12-08MSINGLE 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
11.886.8696.60.070.0710.33.463868
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)
11.81.990.50.2822.42

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 REPLACEMENTTHROUGHOUT5KF11.886.8660566328796.60.1590.1570.198RANDOM19.34
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]
-0.17-0.38-0.450.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.883
r_dihedral_angle_4_deg19.961
r_dihedral_angle_3_deg15.341
r_dihedral_angle_1_deg7.075
r_long_range_B_refined6.967
r_long_range_B_other6.966
r_scangle_other5.504
r_scbond_it3.655
r_scbond_other3.655
r_mcangle_it2.794
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.883
r_dihedral_angle_4_deg19.961
r_dihedral_angle_3_deg15.341
r_dihedral_angle_1_deg7.075
r_long_range_B_refined6.967
r_long_range_B_other6.966
r_scangle_other5.504
r_scbond_it3.655
r_scbond_other3.655
r_mcangle_it2.794
r_mcangle_other2.793
r_mcbond_it2.05
r_mcbond_other2.05
r_angle_refined_deg1.821
r_angle_other_deg0.843
r_chiral_restr0.335
r_bond_refined_d0.013
r_gen_planes_refined0.009
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 Atoms5218
Nucleic Acid Atoms
Solvent Atoms509
Heterogen Atoms247

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing