5KGH

X-ray structure of a glucosamine N-Acetyltransferase from Clostridium acetobutylicum, mutant Y297F


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52938-11% PEG-8000, 100 mM homopipes,
Crystal Properties
Matthews coefficientSolvent content
2.448.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.294α = 90
b = 65.941β = 106.57
c = 90.449γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 1352016-01-17MSINGLE 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
11.85098.10.080.0811.36.666070
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)
11.81.994.60.3792.23

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 REPLACEMENTTHROUGHOUT5KF11.85062715334698.060.206930.204660.24887RANDOM26.281
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]
-0.050.46-0.60.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.98
r_dihedral_angle_4_deg17.39
r_dihedral_angle_3_deg15.767
r_dihedral_angle_1_deg7.501
r_long_range_B_refined6.371
r_long_range_B_other6.37
r_scangle_other4.709
r_mcangle_it3.268
r_mcangle_other3.268
r_scbond_it3.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.98
r_dihedral_angle_4_deg17.39
r_dihedral_angle_3_deg15.767
r_dihedral_angle_1_deg7.501
r_long_range_B_refined6.371
r_long_range_B_other6.37
r_scangle_other4.709
r_mcangle_it3.268
r_mcangle_other3.268
r_scbond_it3.107
r_scbond_other3.105
r_mcbond_it2.334
r_mcbond_other2.333
r_angle_refined_deg1.775
r_angle_other_deg0.87
r_chiral_restr0.104
r_bond_refined_d0.009
r_gen_planes_refined0.007
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 Atoms5195
Nucleic Acid Atoms
Solvent Atoms419
Heterogen Atoms165

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing