5C9P

Crystal structure of recombinant PLL lectin complexed with L-fucose from Photorhabdus luminescens at 1.75 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5C9O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5290.150.1 M Tris-HCl, 2.5 % ethanol, pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.9558.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.783α = 90
b = 87.717β = 90
c = 158.194γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918BESSY14.1

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
11.7545.711000.0914.16.751368
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)
11.751.8499.90.4623.46.6

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 REPLACEMENTTHROUGHOUT5C9O1.7539.148756260899.960.143630.14170.18111RANDOM18.931
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]
1.82-0.8-1.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.261
r_dihedral_angle_4_deg15.698
r_dihedral_angle_3_deg11.996
r_dihedral_angle_1_deg8.158
r_long_range_B_refined6.387
r_long_range_B_other5.956
r_scangle_other4.427
r_scbond_it3.092
r_scbond_other3.085
r_mcangle_other3.066
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.261
r_dihedral_angle_4_deg15.698
r_dihedral_angle_3_deg11.996
r_dihedral_angle_1_deg8.158
r_long_range_B_refined6.387
r_long_range_B_other5.956
r_scangle_other4.427
r_scbond_it3.092
r_scbond_other3.085
r_mcangle_other3.066
r_mcangle_it3.064
r_mcbond_it2.164
r_mcbond_other2.145
r_angle_refined_deg2.124
r_angle_other_deg1.176
r_chiral_restr0.154
r_bond_refined_d0.024
r_gen_planes_refined0.013
r_bond_other_d0.003
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 Atoms2750
Nucleic Acid Atoms
Solvent Atoms384
Heterogen Atoms93

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing