6LGI

Bombyx mori GH13 sucrose hydrolase mutant E322Q covalent intermediate complexed with fructose


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29310% PEG 3350, 0.2 M magnesium acetate, 10 mM alpha-glucopyranosyl fluoride, 10 mM fructose
Crystal Properties
Matthews coefficientSolvent content
2.6954.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.405α = 90
b = 147.055β = 90
c = 153.544γ = 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
11.65099.70.0610.99916.96.4194405
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)
11.61.691000.650.8332.66.6

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 REPLACEMENTTHROUGHOUT5BRQ1.642.04184741954999.560.17950.17810.2071RANDOM29.143
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_deg32.636
r_dihedral_angle_4_deg17.462
r_dihedral_angle_3_deg13.276
r_dihedral_angle_1_deg7.236
r_angle_refined_deg1.78
r_angle_other_deg1.491
r_chiral_restr0.095
r_bond_refined_d0.013
r_gen_planes_refined0.012
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.636
r_dihedral_angle_4_deg17.462
r_dihedral_angle_3_deg13.276
r_dihedral_angle_1_deg7.236
r_angle_refined_deg1.78
r_angle_other_deg1.491
r_chiral_restr0.095
r_bond_refined_d0.013
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9302
Nucleic Acid Atoms
Solvent Atoms983
Heterogen Atoms85

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing