2BS6 | pdb_00002bs6

LECTIN FROM RALSTONIA SOLANACEARUM COMPLEXED WITH XYLOGLUCAN FRAGMENT


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherCOMPLEX WITH SELENIO SUGAR (WATER, LIGAND REMOVED

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROPRSL/FUCOSE CRYSTALS WERE PREPARED BY HANGING DROPS METHODS USING 1.5M NH42(S04) AND SOAKED IN 2.7 MG/ML XXFG SOLUTION
Crystal Properties
Matthews coefficientSolvent content
2.345

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.127α = 90
b = 64.127β = 90
c = 128.121γ = 90
Symmetry
Space GroupP 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL MIRROR2005-01-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.864.1599.70.1114.98.352422114.3
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)
11.81.8596.70.473.16.2

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTCOMPLEX WITH SELENIO SUGAR (WATER, LIGAND REMOVED1.864.1525520129999.70.1480.1460.160.1880.2RANDOM11.34
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]
-0.019-0.0190.038
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.478
r_dihedral_angle_3_deg10.845
r_dihedral_angle_1_deg7.032
r_dihedral_angle_4_deg5.099
r_scangle_it3.076
r_scbond_it2.27
r_angle_refined_deg1.833
r_mcangle_it1.66
r_mcbond_it1.336
r_angle_other_deg0.797
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.478
r_dihedral_angle_3_deg10.845
r_dihedral_angle_1_deg7.032
r_dihedral_angle_4_deg5.099
r_scangle_it3.076
r_scbond_it2.27
r_angle_refined_deg1.833
r_mcangle_it1.66
r_mcbond_it1.336
r_angle_other_deg0.797
r_nbd_other0.209
r_nbtor_refined0.181
r_xyhbond_nbd_refined0.181
r_nbd_refined0.178
r_symmetry_vdw_other0.163
r_symmetry_vdw_refined0.15
r_chiral_restr0.149
r_symmetry_hbond_refined0.145
r_nbtor_other0.089
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2024
Nucleic Acid Atoms
Solvent Atoms334
Heterogen Atoms162

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing