2P37 | pdb_00002p37

Crystal structure of a lectin from Canavalia maritima seeds (CML) in complex with man1-3man-OMe


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72934.5-6.5M sodium formate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.244.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.391α = 90
b = 69.391β = 90
c = 161.298γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 130 mmMSINGLE 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
12.133.920.0910.09115.84.250169
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)
2.12.1550.2960.29634

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.133.9247577252498.890.190360.186820.190.255280.25RANDOM22.465
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_deg36.83
r_dihedral_angle_3_deg18.023
r_dihedral_angle_4_deg17.877
r_dihedral_angle_1_deg12.296
r_scangle_it3.901
r_scbond_it2.788
r_angle_refined_deg2.218
r_mcangle_it1.828
r_mcbond_it1.085
r_nbtor_refined0.318
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.83
r_dihedral_angle_3_deg18.023
r_dihedral_angle_4_deg17.877
r_dihedral_angle_1_deg12.296
r_scangle_it3.901
r_scbond_it2.788
r_angle_refined_deg2.218
r_mcangle_it1.828
r_mcbond_it1.085
r_nbtor_refined0.318
r_symmetry_vdw_refined0.248
r_nbd_refined0.24
r_symmetry_hbond_refined0.203
r_chiral_restr0.168
r_xyhbond_nbd_refined0.168
r_metal_ion_refined0.141
r_bond_refined_d0.021
r_gen_planes_refined0.009
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 Atoms7090
Nucleic Acid Atoms
Solvent Atoms350
Heterogen Atoms104

Software

Software
Software NamePurpose
REFMACrefinement