6JW8

The crystal structure of KanD2 in complex with NADH and 3"-deamino-3"-hydroxykanamycin B


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293PEG 8000, imidazole, calcium acetate, NADH, 3"-deamino-3"-hydroxykanamycin B
Crystal Properties
Matthews coefficientSolvent content
3.3262.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.761α = 90
b = 119.761β = 90
c = 132.904γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2018-01-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0000Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.4501000.08231.59.943656
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)
12.42.4499.50.7132.57.9

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 REPLACEMENTTHROUGHOUT4H3V2.444.3441453212499.940.221630.22010.2519RANDOM69.803
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]
0.970.970.97-3.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.434
r_dihedral_angle_4_deg20.308
r_dihedral_angle_3_deg18.654
r_dihedral_angle_1_deg6.692
r_angle_refined_deg1.995
r_angle_other_deg1.173
r_chiral_restr0.1
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_bond_other_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.434
r_dihedral_angle_4_deg20.308
r_dihedral_angle_3_deg18.654
r_dihedral_angle_1_deg6.692
r_angle_refined_deg1.995
r_angle_other_deg1.173
r_chiral_restr0.1
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_bond_other_d0.006
r_gen_planes_other0.006
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5172
Nucleic Acid Atoms
Solvent Atoms30
Heterogen Atoms121

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing