6LGD

Bombyx mori GH13 sucrose hydrolase complexed with 1,4-dideoxy-1,4-imino-D-arabinitol


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, 10 mM 1,4-dideoxy-1,4-imino-D-arabinitol
Crystal Properties
Matthews coefficientSolvent content
2.7254.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.054α = 90
b = 146.444β = 90
c = 153.291γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2019-11-24MSINGLE 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)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
11.75501000.0740.99915.46.6148203
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)
11.751.841000.8890.7552.26.7

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 REPLACEMENTTHROUGHOUT5BRQ1.7548.29140585733599.950.16320.16210.1837RANDOM28.54
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]
0.48-1.561.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.81
r_dihedral_angle_4_deg15.65
r_dihedral_angle_3_deg12.617
r_dihedral_angle_1_deg6.956
r_angle_other_deg1.314
r_angle_refined_deg1.301
r_chiral_restr0.063
r_gen_planes_refined0.006
r_bond_refined_d0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.81
r_dihedral_angle_4_deg15.65
r_dihedral_angle_3_deg12.617
r_dihedral_angle_1_deg6.956
r_angle_other_deg1.314
r_angle_refined_deg1.301
r_chiral_restr0.063
r_gen_planes_refined0.006
r_bond_refined_d0.005
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 Atoms1021
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
MOLREPphasing