2P1S

Crystal structure of the C-terminal lobe of bovine lactoferrin complexed with O-alpha-D-Glucopyranosyl-(1 3)-alpha-D-fructofuranosyl- (2 1)- alpha-D-glucopyranoside at 1.93 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2O1L 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.82980.1M HEPES, 0.2M ZnSO4, 20% PEG monomethyl ether, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6653.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.155α = 90
b = 50.425β = 107.7
c = 65.883γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray292IMAGE PLATEMAR scanner 345 mm platemirror2007-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54132

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.9363.2594.12817226745
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.93283

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 REPLACEMENTTHROUGHOUT2O1L1.9363.252817226745141394.080.174410.170320.21652RANDOM33.326
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]
0.83-1.43-0.85-0.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.43
r_scangle_it4.857
r_dihedral_angle_1_deg4.691
r_scbond_it2.896
r_mcangle_it2.126
r_angle_refined_deg1.689
r_mcbond_it1.133
r_symmetry_vdw_refined0.262
r_nbd_refined0.232
r_symmetry_hbond_refined0.176
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.43
r_scangle_it4.857
r_dihedral_angle_1_deg4.691
r_scbond_it2.896
r_mcangle_it2.126
r_angle_refined_deg1.689
r_mcbond_it1.133
r_symmetry_vdw_refined0.262
r_nbd_refined0.232
r_symmetry_hbond_refined0.176
r_xyhbond_nbd_refined0.166
r_chiral_restr0.117
r_metal_ion_refined0.061
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2594
Nucleic Acid Atoms
Solvent Atoms324
Heterogen Atoms149

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
AUTOMARdata reduction
SCALEPACKdata scaling
AMoREphasing