6ZPW

Structure of Unliganded MgGH51 a-L-Arabinofuranosidase Crystal Type 2


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29310 mg/mL MgGH51 in 10 mM NaOAc pH 5.5, 100 mM NaCl mixed 2:1 with 2.4 M (NH4)2SO4, 0.1 M NaOAc, pH 6, 20% glycerol

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.953α = 90
b = 125.838β = 90
c = 161.226γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2019-09-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
11.32980.74399.90.0350.9999.68265496
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)
11.331.35980.7270.5211.16.8

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-VALUE6ZPS1.32980.7432654731311899.8490.1310.13030.151115.393
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]
-0.249-0.3410.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.039
r_dihedral_angle_4_deg15.701
r_dihedral_angle_3_deg11.315
r_dihedral_angle_1_deg7.043
r_rigid_bond_restr3.555
r_scangle_it3.111
r_scangle_other3.111
r_lrange_it3.027
r_lrange_other2.775
r_scbond_it2.614
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.039
r_dihedral_angle_4_deg15.701
r_dihedral_angle_3_deg11.315
r_dihedral_angle_1_deg7.043
r_rigid_bond_restr3.555
r_scangle_it3.111
r_scangle_other3.111
r_lrange_it3.027
r_lrange_other2.775
r_scbond_it2.614
r_scbond_other2.614
r_angle_refined_deg1.931
r_mcangle_it1.724
r_mcangle_other1.724
r_angle_other_deg1.655
r_mcbond_it1.569
r_mcbond_other1.505
r_nbd_refined0.209
r_symmetry_xyhbond_nbd_refined0.192
r_nbtor_refined0.18
r_symmetry_nbd_other0.178
r_nbd_other0.167
r_xyhbond_nbd_refined0.136
r_chiral_restr0.116
r_symmetry_nbd_refined0.107
r_symmetry_nbtor_other0.086
r_bond_refined_d0.014
r_gen_planes_refined0.013
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4788
Nucleic Acid Atoms
Solvent Atoms719
Heterogen Atoms229

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
DIALSdata scaling
MOLREPphasing