3AUS | pdb_00003aus

Crystal structure of Bacillus megaterium glucose dehydrogenase 4 in ligand-free form


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.1M sodium cacodylate pH 6.5, 0.2M magnesium chloride, 50% PEG 200, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1743.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.06α = 90
b = 128.531β = 110.7
c = 64.717γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702010-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.00000Photon FactoryAR-NE3A

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
125098.50.0522.353.83307330.8
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)
122.0892.10.2784.863.43074

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT232.1331392166298.10.207920.205250.210.259310.26RANDOM39.076
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]
3.190.51-0.46-2.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.797
r_dihedral_angle_4_deg22.871
r_dihedral_angle_3_deg14.226
r_dihedral_angle_1_deg5.851
r_scangle_it2.689
r_scbond_it1.695
r_angle_refined_deg1.196
r_mcangle_it1.168
r_mcbond_it0.654
r_chiral_restr0.086
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3974
Nucleic Acid Atoms
Solvent Atoms164
Heterogen Atoms

Software

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