6ZPY

Structure of Arabinose-Bound MgGH51 a-L-Arabinofuranosidase Crystal Type 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6ZPS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529310 mg/mL MgGH51 in 10 mM NaOAc, pH 5.5, 100 mM NaCl mixed 2:1 with 20% PEG 3350, 0.1 M Bis-Tris-HCl, pH 6.5, 0.2 M NaNO3
Crystal Properties
Matthews coefficientSolvent content
2.550.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.708α = 90
b = 65.043β = 90
c = 174.122γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2019-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9119DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.2765.0498.50.040.9968.77.917635711.14
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.271.2997.30.3740.7640.87.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6ZPS1.2756.544176207865298.3910.1410.13940.178814.949
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]
-0.470.705-0.235
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.103
r_dihedral_angle_4_deg16.086
r_dihedral_angle_3_deg11.616
r_dihedral_angle_1_deg7.192
r_rigid_bond_restr3.024
r_lrange_it2.801
r_scangle_it2.568
r_scangle_other2.551
r_lrange_other2.517
r_scbond_it2.226
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.103
r_dihedral_angle_4_deg16.086
r_dihedral_angle_3_deg11.616
r_dihedral_angle_1_deg7.192
r_rigid_bond_restr3.024
r_lrange_it2.801
r_scangle_it2.568
r_scangle_other2.551
r_lrange_other2.517
r_scbond_it2.226
r_scbond_other2.214
r_angle_refined_deg1.833
r_mcangle_it1.745
r_mcangle_other1.745
r_angle_other_deg1.641
r_mcbond_it1.5
r_mcbond_other1.5
r_nbd_refined0.207
r_nbtor_refined0.187
r_symmetry_nbd_other0.184
r_symmetry_xyhbond_nbd_refined0.146
r_xyhbond_nbd_refined0.136
r_nbd_other0.135
r_chiral_restr0.105
r_symmetry_nbtor_other0.089
r_symmetry_nbd_refined0.033
r_bond_refined_d0.015
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4775
Nucleic Acid Atoms
Solvent Atoms818
Heterogen Atoms150

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing