5U4Q

1.5 Angstrom Resolution Crystal Structure of NAD-Dependent Epimerase from Klebsiella pneumoniae in Complex with NAD.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.3295Protein: 7.6 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3); Screen: PEGs II (E10), 0.2M Ammonium sulfate, 20% (w/v) PEG 4000.
Crystal Properties
Matthews coefficientSolvent content
2.1442.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.239α = 90
b = 55.845β = 93.21
c = 97.318γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDC(111)2015-04-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

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
11.53099.90.0710.07124.84.3102114-320.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.531000.6290.82.34.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.529.2197040503399.420.181890.18040.2114RANDOM27.325
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]
0.270.490.78-1.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.568
r_dihedral_angle_4_deg11.29
r_dihedral_angle_3_deg10.041
r_long_range_B_refined5.744
r_long_range_B_other5.651
r_scangle_other3.827
r_dihedral_angle_1_deg3.817
r_mcangle_it3.027
r_mcangle_other3.027
r_scbond_it2.509
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.568
r_dihedral_angle_4_deg11.29
r_dihedral_angle_3_deg10.041
r_long_range_B_refined5.744
r_long_range_B_other5.651
r_scangle_other3.827
r_dihedral_angle_1_deg3.817
r_mcangle_it3.027
r_mcangle_other3.027
r_scbond_it2.509
r_scbond_other2.509
r_mcbond_it1.991
r_mcbond_other1.979
r_angle_refined_deg1.444
r_angle_other_deg0.873
r_chiral_restr0.086
r_gen_planes_refined0.023
r_gen_planes_other0.019
r_bond_refined_d0.01
r_bond_other_d0.001
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 Atoms4953
Nucleic Acid Atoms
Solvent Atoms583
Heterogen Atoms89

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing