7DVA

Structure of wild type Bt4394, a GH20 family sulfoglycosidase, in complex with 6S-GlcNAc


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3RCN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP28210 mM of 4MU-6S-GlcNAc with 10 mg/mL protein in the buffer of 25 mM PH 8.0, =300 mM NaCl was mixed with 0.1 M BICINE, pH 8.5, 20 % (w/v) PEG 10000 at 1:1 to carry on co-crystallization.
Crystal Properties
Matthews coefficientSolvent content
2.1342.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.5α = 90
b = 125.596β = 90.631
c = 84.64γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2019-04-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.979191SSRFBL17U1

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
11.5570.1997.40.0970.99611.56.8145268
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)
11.551.581.0050.5842

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3rcn1.5550.483145227746797.2240.1440.14170.184422.979
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]
-0.4490.3281.723-1.281
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.207
r_dihedral_angle_4_deg18.414
r_dihedral_angle_3_deg12.863
r_dihedral_angle_1_deg6.466
r_lrange_it3.44
r_scangle_it3.069
r_scbond_it2.625
r_mcangle_it2.284
r_mcbond_it1.762
r_rigid_bond_restr1.467
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.207
r_dihedral_angle_4_deg18.414
r_dihedral_angle_3_deg12.863
r_dihedral_angle_1_deg6.466
r_lrange_it3.44
r_scangle_it3.069
r_scbond_it2.625
r_mcangle_it2.284
r_mcbond_it1.762
r_rigid_bond_restr1.467
r_angle_refined_deg1.217
r_nbtor_refined0.315
r_symmetry_nbd_refined0.24
r_nbd_refined0.202
r_symmetry_xyhbond_nbd_refined0.131
r_xyhbond_nbd_refined0.113
r_chiral_restr0.092
r_gen_planes_refined0.006
r_bond_refined_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8495
Nucleic Acid Atoms
Solvent Atoms566
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction