6A3J

Levoglucosan dehydrogenase, complex with NADH and L-sorbose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4H3V 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6293MES-NaOH, PEG3000, PEG 200, NADH, L-sorbose
Crystal Properties
Matthews coefficientSolvent content
2.0141.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.186α = 90
b = 93.448β = 101.42
c = 100.882γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2016-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-1A1.000Photon FactoryBL-1A

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
11.9501000.10313.83.8114792
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)
11.91.9399.90.720.9361.73.7

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 REPLACEMENTTHROUGHOUT4H3V1.949.49108882588699.80.168420.166330.20684RANDOM28.603
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.032
r_dihedral_angle_4_deg14.588
r_dihedral_angle_3_deg13.938
r_dihedral_angle_1_deg7.224
r_long_range_B_refined4.858
r_long_range_B_other4.808
r_scangle_other3.676
r_mcangle_it2.524
r_mcangle_other2.524
r_scbond_it2.513
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.032
r_dihedral_angle_4_deg14.588
r_dihedral_angle_3_deg13.938
r_dihedral_angle_1_deg7.224
r_long_range_B_refined4.858
r_long_range_B_other4.808
r_scangle_other3.676
r_mcangle_it2.524
r_mcangle_other2.524
r_scbond_it2.513
r_scbond_other2.513
r_mcbond_it1.818
r_mcbond_other1.818
r_angle_refined_deg1.433
r_angle_other_deg0.992
r_chiral_restr0.069
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.002
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 Atoms11495
Nucleic Acid Atoms
Solvent Atoms767
Heterogen Atoms216

Software

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