7P4D

Crystal Structure of Agd31B, alpha-transglucosylase in Glycoside Hydrolase Family 31, in complex with covalent Cyclophellitol Sulfamidate probe KK130


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4B9Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72931.8 M AMMONIUM SULFATE, 0.1 M HEPES (PH 7.0), 2% PEG400
Crystal Properties
Matthews coefficientSolvent content
3.2462.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 197.076α = 90
b = 197.076β = 90
c = 102.149γ = 120
Symmetry
Space GroupP 6 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2019-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97950DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.8598.541000.1330.1360.0270.99914.224.799190
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.882.6852.7410.5450.6961.4

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-VALUE4b9y1.8598.53899175458399.9470.190.18840.221639.213
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]
-1.224-0.612-1.2243.972
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.51
r_dihedral_angle_4_deg16.169
r_dihedral_angle_3_deg14.676
r_lrange_it7.942
r_lrange_other7.914
r_dihedral_angle_1_deg7.687
r_scangle_it6.377
r_scangle_other6.263
r_mcangle_it4.544
r_mcangle_other4.544
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.51
r_dihedral_angle_4_deg16.169
r_dihedral_angle_3_deg14.676
r_lrange_it7.942
r_lrange_other7.914
r_dihedral_angle_1_deg7.687
r_scangle_it6.377
r_scangle_other6.263
r_mcangle_it4.544
r_mcangle_other4.544
r_scbond_it4.244
r_scbond_other4.158
r_mcbond_it3.438
r_mcbond_other3.437
r_angle_other_deg2.326
r_angle_refined_deg1.62
r_chiral_restr_other0.963
r_symmetry_nbd_other0.217
r_nbd_other0.211
r_nbd_refined0.199
r_symmetry_xyhbond_nbd_refined0.195
r_nbtor_refined0.172
r_xyhbond_nbd_refined0.157
r_symmetry_nbd_refined0.146
r_chiral_restr0.08
r_symmetry_nbtor_other0.078
r_bond_other_d0.035
r_symmetry_xyhbond_nbd_other0.032
r_gen_planes_other0.014
r_bond_refined_d0.01
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6237
Nucleic Acid Atoms
Solvent Atoms485
Heterogen Atoms83

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
REFMACphasing