6A3I

Levoglucosan dehydrogenase, complex with NADH and levoglucosan


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6293MES-NaOH, PEG 3000, PEG 200, NADH, levoglucosan
Crystal Properties
Matthews coefficientSolvent content
1.9537

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.725α = 90
b = 92.354β = 104.48
c = 100.563γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2016-11-05MSINGLE 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
12.45099.50.08316.13.351934
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)
12.42.4499.70.520.9592.43.4

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 REPLACEMENTTHROUGHOUT4H3V2.4134.8449298261898.550.218610.214520.29705RANDOM63.786
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]
0.020.01-0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.619
r_dihedral_angle_3_deg18.569
r_dihedral_angle_4_deg16.446
r_long_range_B_refined8.459
r_long_range_B_other8.459
r_dihedral_angle_1_deg7.683
r_mcangle_it6.479
r_mcangle_other6.478
r_scangle_other5.818
r_mcbond_it4.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.619
r_dihedral_angle_3_deg18.569
r_dihedral_angle_4_deg16.446
r_long_range_B_refined8.459
r_long_range_B_other8.459
r_dihedral_angle_1_deg7.683
r_mcangle_it6.479
r_mcangle_other6.478
r_scangle_other5.818
r_mcbond_it4.44
r_mcbond_other4.44
r_scbond_it3.956
r_scbond_other3.949
r_angle_refined_deg1.248
r_angle_other_deg0.816
r_chiral_restr0.057
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.003
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 Atoms11366
Nucleic Acid Atoms
Solvent Atoms61
Heterogen Atoms91

Software

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