8JEB

Crystal structure of CGL1 from Crassostrea gigas, mannotetraose-bound form (CGL1/Man(alpha)1-2Man(alpha)1-2Man(alpha)1-6Man)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5IDB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2930.2 M magnesium acetate, 0.1 M sodium cacodylate (pH 6.5), 20% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.2545.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.4α = 90
b = 82.495β = 90
c = 44.201γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90PIXELDECTRIS PILATUS3 S 6M2021-11-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.344.20199.20.053122.912.568918
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.320.7470.837

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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-VALUE1.344.20168858346799.1830.1570.15640.174514.566
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]
-0.002-0.0020.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.681
r_dihedral_angle_3_deg12.654
r_dihedral_angle_1_deg7.398
r_lrange_it4.867
r_lrange_other4.812
r_scangle_it4.286
r_scangle_other4.285
r_dihedral_angle_2_deg4.192
r_scbond_it3.005
r_scbond_other3.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.681
r_dihedral_angle_3_deg12.654
r_dihedral_angle_1_deg7.398
r_lrange_it4.867
r_lrange_other4.812
r_scangle_it4.286
r_scangle_other4.285
r_dihedral_angle_2_deg4.192
r_scbond_it3.005
r_scbond_other3.004
r_angle_refined_deg1.655
r_mcangle_it1.483
r_mcangle_other1.483
r_mcbond_it1.092
r_mcbond_other1.057
r_symmetry_nbd_refined0.735
r_angle_other_deg0.579
r_chiral_restr0.313
r_nbd_refined0.256
r_symmetry_nbd_other0.219
r_nbd_other0.194
r_nbtor_refined0.177
r_symmetry_xyhbond_nbd_refined0.162
r_xyhbond_nbd_refined0.125
r_symmetry_nbtor_other0.086
r_metal_ion_refined0.045
r_symmetry_xyhbond_nbd_other0.029
r_bond_refined_d0.012
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 Atoms2180
Nucleic Acid Atoms
Solvent Atoms308
Heterogen Atoms115

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing