6LGE

Bombyx mori GH13 sucrose hydrolase complexed with acarbose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5BRQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2938% PEG 3350, 0.2 M magnesium acetate, 2 mM acarbose
Crystal Properties
Matthews coefficientSolvent content
2.6453.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.247α = 90
b = 145.792β = 90
c = 152.857γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 2M2019-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0Photon FactoryAR-NW12A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.75501000.080.99918.712.3147455
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)
11.751.841000.8050.8462.811.9

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 REPLACEMENTTHROUGHOUT5BRQ1.7548.66139957729699.920.19880.19730.2285RANDOM29.698
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]
-0.030.24-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.884
r_dihedral_angle_4_deg16.98
r_dihedral_angle_3_deg13.598
r_dihedral_angle_1_deg7.391
r_angle_refined_deg1.689
r_angle_other_deg1.414
r_chiral_restr0.086
r_bond_refined_d0.011
r_gen_planes_refined0.011
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.884
r_dihedral_angle_4_deg16.98
r_dihedral_angle_3_deg13.598
r_dihedral_angle_1_deg7.391
r_angle_refined_deg1.689
r_angle_other_deg1.414
r_chiral_restr0.086
r_bond_refined_d0.011
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9295
Nucleic Acid Atoms
Solvent Atoms610
Heterogen Atoms94

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing