3K0V

Removal of sugars and sugars-like molecules from the solution by C-lobe of lactoferrin: Crystal structure of the complex of C-lobe with beta-D-glucopyranosyl-(1->4)-beta-D-galactopyranosyl-(1->4)-alpha-D-glucopyranose at 1.9 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IBOpdb entry 3IBO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52980.01M Znso4, 0.1M MES, 25% PEG, Monomethyl Ether 550, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5852.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.81α = 90
b = 50.134β = 107.1
c = 65.545γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray300IMAGE PLATEMARRESEARCHMIRROR2009-04-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.9162.62960.0587.12953829538
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.911.9699.10.1042.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 3IBO1.91622829626864143294.540.208840.206770.23685RANDOM25.247
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]
1.06-0.62-0.93-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.332
r_dihedral_angle_4_deg19.535
r_dihedral_angle_3_deg16.642
r_dihedral_angle_1_deg5.889
r_scangle_it2.51
r_scbond_it1.579
r_angle_refined_deg1.28
r_mcangle_it1.17
r_mcbond_it0.681
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.332
r_dihedral_angle_4_deg19.535
r_dihedral_angle_3_deg16.642
r_dihedral_angle_1_deg5.889
r_scangle_it2.51
r_scbond_it1.579
r_angle_refined_deg1.28
r_mcangle_it1.17
r_mcbond_it0.681
r_nbtor_refined0.303
r_symmetry_hbond_refined0.292
r_symmetry_vdw_refined0.279
r_nbd_refined0.202
r_xyhbond_nbd_refined0.128
r_chiral_restr0.086
r_metal_ion_refined0.034
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2604
Nucleic Acid Atoms
Solvent Atoms415
Heterogen Atoms152

Software

Software
Software NamePurpose
DENZOdata reduction
MOLREPphasing
REFMACrefinement
AUTOMARdata reduction
SCALEPACKdata scaling