8JEA

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


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
2.0439.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.734α = 90
b = 58.674β = 93.657
c = 108.41γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90PIXELDECTRIS PILATUS3 S 6M2021-12-02MSINGLE 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
10.9739.7711000.036128.612.8292966
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)
10.970.991.0210.82

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-VALUE0.9739.7712929281481099.9880.1760.17510.188511.064
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]
-0.001-0.0010.015-0.013
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg18.915
r_rigid_bond_restr15.562
r_dihedral_angle_3_deg12.802
r_dihedral_angle_1_deg7.24
r_dihedral_angle_2_deg4.098
r_lrange_it3.374
r_lrange_other3.341
r_scangle_it2.931
r_scangle_other2.931
r_scbond_other2.929
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg18.915
r_rigid_bond_restr15.562
r_dihedral_angle_3_deg12.802
r_dihedral_angle_1_deg7.24
r_dihedral_angle_2_deg4.098
r_lrange_it3.374
r_lrange_other3.341
r_scangle_it2.931
r_scangle_other2.931
r_scbond_other2.929
r_scbond_it2.928
r_mcangle_it2.221
r_mcangle_other2.221
r_mcbond_it2.142
r_mcbond_other2.142
r_angle_refined_deg1.799
r_angle_other_deg0.993
r_symmetry_nbd_refined0.296
r_nbd_other0.251
r_symmetry_nbd_other0.212
r_nbd_refined0.211
r_nbtor_refined0.179
r_xyhbond_nbd_refined0.14
r_symmetry_xyhbond_nbd_refined0.119
r_symmetry_nbtor_other0.107
r_chiral_restr0.099
r_gen_planes_other0.022
r_bond_refined_d0.014
r_gen_planes_refined0.012
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4360
Nucleic Acid Atoms
Solvent Atoms815
Heterogen Atoms95

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing