6A3G

Levoglucosan dehydrogenase, complex with NADH


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
Crystal Properties
Matthews coefficientSolvent content
2.1241.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.742α = 90
b = 93.787β = 100.97
c = 100.989γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702015-12-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.000Photon FactoryAR-NW12A

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
11.95098.70.10411.43.6114689
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)
11.91.9397.20.7770.9031.43.3

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 REPLACEMENTTHROUGHOUT4H3V1.936.53109019565298.580.170460.168660.20448RANDOM23.468
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]
-0.020.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.773
r_dihedral_angle_4_deg15.073
r_dihedral_angle_3_deg13.329
r_dihedral_angle_1_deg7.151
r_long_range_B_refined4.354
r_long_range_B_other4.308
r_scangle_other3.338
r_scbond_it2.218
r_scbond_other2.218
r_mcangle_it2.188
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.773
r_dihedral_angle_4_deg15.073
r_dihedral_angle_3_deg13.329
r_dihedral_angle_1_deg7.151
r_long_range_B_refined4.354
r_long_range_B_other4.308
r_scangle_other3.338
r_scbond_it2.218
r_scbond_other2.218
r_mcangle_it2.188
r_mcangle_other2.188
r_mcbond_it1.547
r_mcbond_other1.546
r_angle_refined_deg1.423
r_angle_other_deg1.002
r_chiral_restr0.069
r_bond_refined_d0.01
r_gen_planes_refined0.007
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 Atoms11461
Nucleic Acid Atoms
Solvent Atoms749
Heterogen Atoms176

Software

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