2JE9

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


X-RAY DIFFRACTION

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