4H7U

Crystal structure of pyranose dehydrogenase from Agaricus meleagris, wildtype


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JBVPDB ENTRY 2JBV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529850 mM KH2PO4, 5% 2-methyl-2,4-pentanediol, 20% (w/v) polyethylene glycol 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0841

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.938α = 90
b = 74.64β = 90
c = 139.286γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2009-06-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-50.90772MAX III911-5

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.648.799.70.07516.47.37203572035
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.799.80.8412.67.311811

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2JBV1.648.76985769857217799.670.171760.171760.170810.20116RANDOM22.481
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]
-0.54-0.521.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.089
r_dihedral_angle_4_deg20.257
r_dihedral_angle_3_deg12.926
r_dihedral_angle_1_deg6.669
r_angle_refined_deg1.853
r_angle_other_deg1.632
r_chiral_restr0.15
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.089
r_dihedral_angle_4_deg20.257
r_dihedral_angle_3_deg12.926
r_dihedral_angle_1_deg6.669
r_angle_refined_deg1.853
r_angle_other_deg1.632
r_chiral_restr0.15
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4375
Nucleic Acid Atoms
Solvent Atoms538
Heterogen Atoms101

Software

Software
Software NamePurpose
MAR345data collection
BALBESphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling