7WJD

Crystal structure of Lactococcus lactis subsp. cremoris GH31 alpha-1,3-glucosidase mutant D394A in complex with nigerotriose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7WJA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729313% PEG 3350, 400 mM ammonium citrate buffer (pH 7.0), 10 mM nigerotriose
Crystal Properties
Matthews coefficientSolvent content
3.3763.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.97α = 90
b = 151.97β = 90
c = 177.671γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 2M2021-06-05MSINGLE 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
11.8501000.072130.519.6111675
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)
11.81.91001.5050.8412.620.2

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-VALUE7WJA1.847.948111610548799.9730.1770.17570.194435.264
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]
0.4830.2420.483-1.568
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.56
r_dihedral_angle_3_deg13.005
r_dihedral_angle_4_deg12.221
r_dihedral_angle_1_deg7.403
r_lrange_it5.96
r_lrange_other5.941
r_scangle_it5.31
r_scangle_other5.309
r_scbond_it3.658
r_scbond_other3.658
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.56
r_dihedral_angle_3_deg13.005
r_dihedral_angle_4_deg12.221
r_dihedral_angle_1_deg7.403
r_lrange_it5.96
r_lrange_other5.941
r_scangle_it5.31
r_scangle_other5.309
r_scbond_it3.658
r_scbond_other3.658
r_mcangle_other3.316
r_mcangle_it3.315
r_mcbond_it2.726
r_mcbond_other2.721
r_angle_refined_deg1.595
r_angle_other_deg1.421
r_nbd_refined0.204
r_nbd_other0.182
r_nbtor_refined0.178
r_symmetry_nbd_refined0.174
r_symmetry_nbd_other0.173
r_xyhbond_nbd_refined0.126
r_chiral_restr0.081
r_symmetry_nbtor_other0.077
r_symmetry_xyhbond_nbd_refined0.069
r_symmetry_xyhbond_nbd_other0.03
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5988
Nucleic Acid Atoms
Solvent Atoms480
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
Cootmodel building