5KGA

X-ray structure of a glucosamine N-Acetyltransferase from Clostridium acetobutylicum, mutant D287N, in complex with N-acetylglucosamine


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, 5 mM CoA, 20 mM N-acetylglucosamine
Crystal Properties
Matthews coefficientSolvent content
2.3146.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63α = 90
b = 65.6β = 107
c = 89.9γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 1352015-12-01MSINGLE 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
11.95098.50.080.082.14.254576
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)
11.9295.60.3892.12.5

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 REPLACEMENTTHROUGHOUT5kf11.95051862271498.480.172640.170020.22385RANDOM20.047
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]
-0.5-0.4-0.350.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.434
r_dihedral_angle_4_deg15.788
r_dihedral_angle_3_deg15.315
r_dihedral_angle_1_deg6.92
r_long_range_B_refined6.403
r_long_range_B_other6.403
r_scangle_other4.303
r_scbond_it2.706
r_scbond_other2.706
r_mcangle_it2.433
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.434
r_dihedral_angle_4_deg15.788
r_dihedral_angle_3_deg15.315
r_dihedral_angle_1_deg6.92
r_long_range_B_refined6.403
r_long_range_B_other6.403
r_scangle_other4.303
r_scbond_it2.706
r_scbond_other2.706
r_mcangle_it2.433
r_mcangle_other2.433
r_angle_refined_deg1.85
r_mcbond_other1.595
r_mcbond_it1.594
r_angle_other_deg0.897
r_chiral_restr0.233
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 Atoms5216
Nucleic Acid Atoms
Solvent Atoms575
Heterogen Atoms222

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing