5H4S

Crystal structure of a rhamnose-binding lectin SUL-I from the toxopneustid sea urchin Toxopneustes pileolus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZX2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2930.2M Lithium sulfate, 0.1M Phosphate-citrate (pH4.2), 20% PEG 1000, 0.05% DDM
Crystal Properties
Matthews coefficientSolvent content
2.1943.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.76α = 90
b = 44.21β = 124.08
c = 71.84γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATERIGAKU RAXIS IV++2014-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.829.899.820.13.524749

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT2ZX21.829.7523467126099.790.159060.15650.20523RANDOM21.522
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.318
r_dihedral_angle_4_deg17.798
r_dihedral_angle_3_deg14.34
r_dihedral_angle_1_deg7.474
r_long_range_B_refined7.163
r_long_range_B_other6.815
r_scangle_other4.571
r_scbond_it2.973
r_scbond_other2.964
r_mcangle_other2.925
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.318
r_dihedral_angle_4_deg17.798
r_dihedral_angle_3_deg14.34
r_dihedral_angle_1_deg7.474
r_long_range_B_refined7.163
r_long_range_B_other6.815
r_scangle_other4.571
r_scbond_it2.973
r_scbond_other2.964
r_mcangle_other2.925
r_mcangle_it2.923
r_mcbond_it1.971
r_mcbond_other1.968
r_angle_refined_deg1.897
r_angle_other_deg1.108
r_chiral_restr0.15
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2116
Nucleic Acid Atoms
Solvent Atoms410
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing