2P2K

Crystal structure of a lectin from Canavalia gladiata seeds (CGL) in complex with man1-4man-OMe


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72934.5-6.5 M sodium formate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1542.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.932α = 90
b = 68.932β = 90
c = 160.436γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 130 mm2006-04-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE D03B-MX1LNLSD03B-MX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.9840.0960.0686.88.810.256114
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.980.23323.33.2

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.9839.8456114298399.570.184530.181750.2363RANDOM18.981
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.761
r_dihedral_angle_4_deg18.809
r_dihedral_angle_3_deg17.635
r_dihedral_angle_1_deg9.103
r_scangle_it3.895
r_scbond_it2.739
r_angle_refined_deg2.128
r_mcangle_it1.825
r_mcbond_it1.12
r_symmetry_hbond_refined0.355
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.761
r_dihedral_angle_4_deg18.809
r_dihedral_angle_3_deg17.635
r_dihedral_angle_1_deg9.103
r_scangle_it3.895
r_scbond_it2.739
r_angle_refined_deg2.128
r_mcangle_it1.825
r_mcbond_it1.12
r_symmetry_hbond_refined0.355
r_nbtor_refined0.322
r_symmetry_vdw_refined0.289
r_nbd_refined0.241
r_xyhbond_nbd_refined0.185
r_metal_ion_refined0.167
r_chiral_restr0.158
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7122
Nucleic Acid Atoms
Solvent Atoms471
Heterogen Atoms104

Software

Software
Software NamePurpose
REFMACrefinement