5NPD

Crystal Structure of D412N nucleophile mutant cjAgd31B (alpha-transglucosylase from Glycoside Hydrolase Family 31) in complex with alpha Cyclophellitol Aziridine probe CF021


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
3.0659.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 197.312α = 90
b = 197.312β = 90
c = 102.772γ = 120
Symmetry
Space GroupP 6 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-07-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9795DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.9547.391000.1020.0230.99921.720.185623
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.951.991001.4080.320.8992.620.3

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 REPLACEMENTTHROUGHOUT4b9y1.9547.3981290433199.950.172910.170950.20994RANDOM36.926
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]
-1.78-0.89-1.785.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.763
r_dihedral_angle_4_deg16.579
r_dihedral_angle_3_deg13.792
r_dihedral_angle_1_deg6.757
r_long_range_B_refined6.59
r_long_range_B_other6.589
r_scangle_other5.173
r_scbond_it3.318
r_scbond_other3.318
r_mcangle_it3.273
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.763
r_dihedral_angle_4_deg16.579
r_dihedral_angle_3_deg13.792
r_dihedral_angle_1_deg6.757
r_long_range_B_refined6.59
r_long_range_B_other6.589
r_scangle_other5.173
r_scbond_it3.318
r_scbond_other3.318
r_mcangle_it3.273
r_mcangle_other3.273
r_mcbond_it2.347
r_mcbond_other2.346
r_angle_refined_deg1.604
r_angle_other_deg0.991
r_chiral_restr0.098
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6236
Nucleic Acid Atoms
Solvent Atoms492
Heterogen Atoms90

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing