4CTE

Crystal structure of the catalytic domain of the modular laminarinase ZgLamC mutant E142S in complex with a thio-oligosaccharide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1511% PEG 6000, 100 MM NA ACETATE PH 5.0, 220 MM MGCL2, 4% ISOPROPANOL AND 3% GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
3.1160

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.01α = 90
b = 93.93β = 90
c = 142.28γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-02-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.7948.299.90.0716.84.9722540.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.791.8599.70.692.22.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4CRQ1.848.1166528353699.790.179460.177180.22221RANDOM33.778
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]
-0.260.71-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.377
r_sphericity_free31.585
r_sphericity_bonded21.184
r_dihedral_angle_4_deg19.997
r_dihedral_angle_3_deg10.881
r_dihedral_angle_1_deg5.404
r_rigid_bond_restr2.856
r_angle_refined_deg1.986
r_chiral_restr0.083
r_bond_refined_d0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.377
r_sphericity_free31.585
r_sphericity_bonded21.184
r_dihedral_angle_4_deg19.997
r_dihedral_angle_3_deg10.881
r_dihedral_angle_1_deg5.404
r_rigid_bond_restr2.856
r_angle_refined_deg1.986
r_chiral_restr0.083
r_bond_refined_d0.02
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3682
Nucleic Acid Atoms
Solvent Atoms333
Heterogen Atoms86

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing