6SXS

GH54 a-l-arabinofuranosidase soaked with cyclic sulfate 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
434

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.136α = 90
b = 111.136β = 90
c = 342.742γ = 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
11.85984.0591000.1280.1330.0390.99910.212.168786
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)
11.861.891005.325.541.530.440.512.8

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-VALUE1WD31.85984.05968786333899.730.1830.18170.21540.242
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]
0.8850.4430.885-2.872
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.2
r_dihedral_angle_4_deg21.509
r_dihedral_angle_3_deg11.758
r_dihedral_angle_1_deg8.225
r_lrange_it5.61
r_lrange_other5.591
r_scangle_it5.198
r_scangle_other5.197
r_scbond_it4.036
r_scbond_other4.035
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.2
r_dihedral_angle_4_deg21.509
r_dihedral_angle_3_deg11.758
r_dihedral_angle_1_deg8.225
r_lrange_it5.61
r_lrange_other5.591
r_scangle_it5.198
r_scangle_other5.197
r_scbond_it4.036
r_scbond_other4.035
r_mcangle_other3.688
r_mcangle_it3.686
r_mcbond_it3.102
r_mcbond_other3.059
r_angle_refined_deg1.768
r_angle_other_deg1.463
r_symmetry_nbd_refined0.311
r_nbd_other0.216
r_nbd_refined0.196
r_symmetry_nbd_other0.18
r_nbtor_refined0.174
r_xyhbond_nbd_refined0.129
r_symmetry_xyhbond_nbd_refined0.122
r_symmetry_nbtor_other0.083
r_chiral_restr0.076
r_bond_refined_d0.012
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 Atoms3568
Nucleic Acid Atoms
Solvent Atoms235
Heterogen Atoms131

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing