6SXU

GH51 a-l-arabinofuranosidase soaked with cyclic sulfate inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PZ3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52932:1 protein:well solution. 0.1 M pH 7.5 Tris-HCl buffer, 18% PEG3350, 0.7 M NH4F, 5% 2-propanol
Crystal Properties
Matthews coefficientSolvent content
2.6956.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 178.47α = 90
b = 178.47β = 90
c = 100.411γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-09-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91587DiamondI04-1

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
11.39829.7599.80.0480.99918.76.2235395
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)
11.41.4397.40.6340.7762.36.1

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-VALUE1PZ31.39829.752353941242199.7620.1550.15480.16216.403
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]
0.0520.0260.052-0.167
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.557
r_dihedral_angle_4_deg17.327
r_dihedral_angle_3_deg11.372
r_dihedral_angle_1_deg7.108
r_lrange_it5.47
r_lrange_other5.293
r_scangle_it4.746
r_scangle_other4.745
r_scbond_it3.43
r_scbond_other3.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.557
r_dihedral_angle_4_deg17.327
r_dihedral_angle_3_deg11.372
r_dihedral_angle_1_deg7.108
r_lrange_it5.47
r_lrange_other5.293
r_scangle_it4.746
r_scangle_other4.745
r_scbond_it3.43
r_scbond_other3.43
r_mcangle_other2.684
r_mcangle_it2.681
r_angle_other_deg2.437
r_mcbond_it2.003
r_angle_refined_deg1.996
r_mcbond_other1.996
r_chiral_restr0.468
r_symmetry_nbd_refined0.347
r_nbd_other0.278
r_nbd_refined0.224
r_symmetry_nbd_other0.211
r_nbtor_refined0.176
r_xyhbond_nbd_refined0.135
r_symmetry_xyhbond_nbd_refined0.117
r_symmetry_nbtor_other0.078
r_bond_other_d0.035
r_gen_planes_other0.022
r_bond_refined_d0.017
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7800
Nucleic Acid Atoms
Solvent Atoms911
Heterogen Atoms77

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing