6UAQ

Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei (AmGH128_I)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.6291sodium acetate 0.1 M sodium chloride 1.5 M
Crystal Properties
Matthews coefficientSolvent content
2.5952.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.35α = 90
b = 78.643β = 101.62
c = 46.183γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2016-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE W01B-MX21.033140LNLSW01B-MX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.1545.28940.99811.512.35171671
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.151.220.808

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMIRASTHROUGHOUT1.1545.2886795440398.760.15060.150.1618RANDOM12.728
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]
0.560.42-0.58-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.694
r_dihedral_angle_4_deg11.925
r_dihedral_angle_3_deg10.279
r_dihedral_angle_1_deg6.98
r_mcangle_it4.221
r_mcbond_it3.668
r_mcbond_other3.251
r_angle_other_deg2.44
r_angle_refined_deg2.097
r_chiral_restr0.132
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.694
r_dihedral_angle_4_deg11.925
r_dihedral_angle_3_deg10.279
r_dihedral_angle_1_deg6.98
r_mcangle_it4.221
r_mcbond_it3.668
r_mcbond_other3.251
r_angle_other_deg2.44
r_angle_refined_deg2.097
r_chiral_restr0.132
r_bond_other_d0.036
r_gen_planes_other0.022
r_bond_refined_d0.018
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1813
Nucleic Acid Atoms
Solvent Atoms355
Heterogen Atoms19

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing