4YNU

Crystal structure of Aspergillus flavus FADGDH in complex with D-glucono-1,5-lactone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1CF3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.1 M BisTris, 20-25 % PEG 3350
Crystal Properties
Matthews coefficientSolvent content
1.9537.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.658α = 90
b = 64.877β = 100.46
c = 75.889γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0Photon FactoryBL-5A

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
11.575099.90.05910.63.765992
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)
11.571.697.60.4833221

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 REPLACEMENTTHROUGHOUT1CF31.5739.0262625334799.730.14190.14070.1642RANDOM20.571
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_deg35.56
r_dihedral_angle_4_deg21.04
r_dihedral_angle_3_deg14.18
r_dihedral_angle_1_deg7.316
r_angle_refined_deg1.123
r_angle_other_deg0.642
r_chiral_restr0.079
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.56
r_dihedral_angle_4_deg21.04
r_dihedral_angle_3_deg14.18
r_dihedral_angle_1_deg7.316
r_angle_refined_deg1.123
r_angle_other_deg0.642
r_chiral_restr0.079
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4324
Nucleic Acid Atoms
Solvent Atoms431
Heterogen Atoms77

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHENIXphasing