2JE9

CRYSTAL STRUCTURE OF RECOMBINANT DIOCLEA GRANDIFLORA LECTIN COMPLEXED WITH 5-BROMO-4-CHLORO-3-INDOLYL-A-D-MANNOSE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DGLPDB ENTRY 1DGL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5CRYSTALS WERE GROWN BY THE HANGING DROP VAPOUR DIFFUSION METHOD USING 15% PEG 4000, 0.1M HEPES, PH 7.5 AND 0.1M LITHIUM SULFATE
Crystal Properties
Matthews coefficientSolvent content
2.6253.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.171α = 90
b = 85.153β = 90
c = 175.741γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2006-03-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
12.172.1799.90.086.94.6639732
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)
12.12.2199.70.32.14

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1DGL2.187.7160684323499.80.190.1870.239RANDOM24.47
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]
0.010.86-0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.534
r_dihedral_angle_3_deg14.486
r_dihedral_angle_4_deg14.171
r_dihedral_angle_1_deg7.709
r_angle_refined_deg1.573
r_nbtor_refined0.299
r_symmetry_hbond_refined0.281
r_symmetry_vdw_refined0.208
r_nbd_refined0.197
r_xyhbond_nbd_refined0.169
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.534
r_dihedral_angle_3_deg14.486
r_dihedral_angle_4_deg14.171
r_dihedral_angle_1_deg7.709
r_angle_refined_deg1.573
r_nbtor_refined0.299
r_symmetry_hbond_refined0.281
r_symmetry_vdw_refined0.208
r_nbd_refined0.197
r_xyhbond_nbd_refined0.169
r_chiral_restr0.109
r_metal_ion_refined0.083
r_bond_refined_d0.015
r_gen_planes_refined0.006
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms7235
Nucleic Acid Atoms
Solvent Atoms441
Heterogen Atoms135

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing