6ZPZ

Structure of a-l-AraCS-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
2.754.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 191.63α = 90
b = 58.09β = 90
c = 65.71γ = 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
11.7158.1298.80.0520.9978.77.57987121.04
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)
11.711.7498.50.6940.4196.7

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-VALUE6ZPS1.7155.65479795399199.4130.1890.18670.224523.46
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]
-0.9891.04-0.051
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.363
r_dihedral_angle_4_deg13.683
r_dihedral_angle_3_deg12.084
r_dihedral_angle_1_deg7.601
r_lrange_it4.033
r_lrange_other3.981
r_scangle_it3.17
r_scangle_other3.17
r_scbond_it2.258
r_scbond_other2.255
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.363
r_dihedral_angle_4_deg13.683
r_dihedral_angle_3_deg12.084
r_dihedral_angle_1_deg7.601
r_lrange_it4.033
r_lrange_other3.981
r_scangle_it3.17
r_scangle_other3.17
r_scbond_it2.258
r_scbond_other2.255
r_mcangle_it2.208
r_mcangle_other2.208
r_angle_refined_deg1.746
r_mcbond_it1.736
r_mcbond_other1.735
r_angle_other_deg1.506
r_symmetry_xyhbond_nbd_refined0.321
r_nbd_refined0.207
r_symmetry_nbd_other0.197
r_nbd_other0.187
r_nbtor_refined0.179
r_xyhbond_nbd_refined0.146
r_symmetry_nbd_refined0.088
r_symmetry_nbtor_other0.087
r_chiral_restr0.078
r_symmetry_xyhbond_nbd_other0.07
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4763
Nucleic Acid Atoms
Solvent Atoms567
Heterogen Atoms138

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing