6SXT

GH54 a-l-arabinofuranosidase soaked with aziridine inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WD3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52932:1 protein:well solution. 0.1 M pH 4.5 sodium acetate buffer, 60% PEG400, 0.3 M (NH4)2SO4
Crystal Properties
Matthews coefficientSolvent content
34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.232α = 90
b = 112.232β = 90
c = 342.73γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2019-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
11.46685.5499.30.1050.1090.0310.9991312.4141273
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)
11.4661.49198.52.983.130.940.3670.710.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1WD31.46684.687141273698099.260.1580.15690.179120.664
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]
0.1540.0770.154-0.499
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.439
r_dihedral_angle_4_deg21.062
r_dihedral_angle_3_deg10.58
r_dihedral_angle_1_deg7.567
r_lrange_it5.344
r_lrange_other5.074
r_scangle_it4.3
r_scangle_other4.299
r_scbond_it3.195
r_scbond_other3.194
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.439
r_dihedral_angle_4_deg21.062
r_dihedral_angle_3_deg10.58
r_dihedral_angle_1_deg7.567
r_lrange_it5.344
r_lrange_other5.074
r_scangle_it4.3
r_scangle_other4.299
r_scbond_it3.195
r_scbond_other3.194
r_angle_other_deg2.577
r_mcangle_it2.241
r_mcangle_other2.241
r_angle_refined_deg1.942
r_mcbond_it1.737
r_mcbond_other1.696
r_symmetry_nbd_refined0.411
r_nbd_other0.389
r_symmetry_nbd_other0.222
r_symmetry_xyhbond_nbd_refined0.221
r_nbd_refined0.219
r_nbtor_refined0.177
r_xyhbond_nbd_refined0.132
r_chiral_restr0.097
r_symmetry_nbtor_other0.089
r_bond_other_d0.037
r_gen_planes_other0.018
r_bond_refined_d0.016
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3578
Nucleic Acid Atoms
Solvent Atoms456
Heterogen Atoms207

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing