5F8Y

Crystal structure of a Crenomytilus grayanus lectin in complex with galactosamine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.2 M imidazole malate, 25%(w/v) PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.6152.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.022α = 90
b = 71.482β = 90
c = 94.065γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11.0NSRRCBL13B1

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
11.73095.40.06240.512.138277
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)
11.71.7691.20.2536.511.1

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 DIFFRACTIONSADTHROUGHOUT1.73035679187593.670.124080.122640.15207RANDOM12.054
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]
-0.240.020.22
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free40.715
r_dihedral_angle_2_deg31.502
r_dihedral_angle_4_deg19.219
r_dihedral_angle_3_deg13.104
r_dihedral_angle_1_deg7.355
r_sphericity_bonded7.237
r_long_range_B_refined4.067
r_rigid_bond_restr3.318
r_long_range_B_other2.865
r_scangle_other2.168
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free40.715
r_dihedral_angle_2_deg31.502
r_dihedral_angle_4_deg19.219
r_dihedral_angle_3_deg13.104
r_dihedral_angle_1_deg7.355
r_sphericity_bonded7.237
r_long_range_B_refined4.067
r_rigid_bond_restr3.318
r_long_range_B_other2.865
r_scangle_other2.168
r_scbond_it1.855
r_scbond_other1.854
r_angle_refined_deg1.553
r_mcangle_other1.481
r_mcangle_it1.475
r_mcbond_it1.233
r_mcbond_other1.231
r_angle_other_deg1.041
r_chiral_restr0.106
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_bond_other_d0.004
r_gen_planes_other0.002
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2390
Nucleic Acid Atoms
Solvent Atoms410
Heterogen Atoms78

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SHELXCDphasing