5KF2

X-ray structure of a glucosamine N-Acetyltransferase from Clostridium acetobutylicum, apo form, pH 8


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
Crystal Properties
Matthews coefficientSolvent content
2.1542.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.79α = 90
b = 43.092β = 120.85
c = 74.43γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 1352015-11-16MSINGLE 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
11.950990.0750.07510.94.725764
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)
11.9297.10.3252.42.8

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 REPLACEMENTTHROUGHOUT5KF11.950244631299990.1740.1710.231RANDOM25.12
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]
-0.16-0.62.43-0.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.228
r_dihedral_angle_4_deg20.687
r_dihedral_angle_3_deg15.602
r_long_range_B_refined7.446
r_long_range_B_other7.445
r_dihedral_angle_1_deg7.417
r_scangle_other5.597
r_mcangle_it3.661
r_mcangle_other3.66
r_scbond_it3.658
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.228
r_dihedral_angle_4_deg20.687
r_dihedral_angle_3_deg15.602
r_long_range_B_refined7.446
r_long_range_B_other7.445
r_dihedral_angle_1_deg7.417
r_scangle_other5.597
r_mcangle_it3.661
r_mcangle_other3.66
r_scbond_it3.658
r_scbond_other3.648
r_mcbond_it2.613
r_mcbond_other2.608
r_angle_refined_deg2.001
r_angle_other_deg0.964
r_chiral_restr0.27
r_bond_refined_d0.011
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 Atoms2620
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms87

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing