6ZQ1

Structure of AraDNJ-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
2.8256.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.803α = 90
b = 65.914β = 90
c = 193.563γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2020-01-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
11.729.8799.90.0280.99915.934.58517213.5
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)
11.71.7399.40.2810.9152.116.3

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-VALUE6ZPS1.729.8785060430399.8940.1960.19460.216519.379
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]
4.511-1.955-2.556
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.749
r_dihedral_angle_4_deg18.266
r_dihedral_angle_3_deg11.878
r_dihedral_angle_1_deg7.697
r_lrange_it4.03
r_lrange_other3.904
r_scangle_it2.857
r_scangle_other2.857
r_mcangle_it2.057
r_mcangle_other2.056
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.749
r_dihedral_angle_4_deg18.266
r_dihedral_angle_3_deg11.878
r_dihedral_angle_1_deg7.697
r_lrange_it4.03
r_lrange_other3.904
r_scangle_it2.857
r_scangle_other2.857
r_mcangle_it2.057
r_mcangle_other2.056
r_scbond_it1.984
r_scbond_other1.984
r_angle_refined_deg1.666
r_mcbond_it1.537
r_mcbond_other1.536
r_angle_other_deg1.435
r_symmetry_xyhbond_nbd_refined0.393
r_nbd_refined0.196
r_symmetry_nbd_other0.185
r_nbtor_refined0.171
r_xyhbond_nbd_refined0.154
r_symmetry_nbd_refined0.108
r_chiral_restr_other0.103
r_nbd_other0.096
r_symmetry_nbtor_other0.083
r_chiral_restr0.081
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4767
Nucleic Acid Atoms
Solvent Atoms545
Heterogen Atoms133

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing