2G93

Ligand recognition site in C-lobe of lactoferrin: Crystal structure of the complex of C-lobe of bovine lactoferrin with methyl alpha-D-mannopyranoside at 1.9 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NKX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.52980.1M MES, PEG monomethyl ether 550, 0.1M ZnSO4, pH 6.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6453.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.411α = 90
b = 50.439β = 107.76
c = 65.956γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATEMARRESEARCHmirror2006-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

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
11.92096.13000229968
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9392.3

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1NKX1.920300022901994994.960.190.189380.188020.22944RANDOM36.018
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]
0.65-0.87-0.43-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.524
r_dihedral_angle_1_deg3.785
r_scangle_it3.449
r_scbond_it2.057
r_mcangle_it1.55
r_angle_refined_deg1.4
r_mcbond_it0.816
r_nbd_refined0.226
r_symmetry_vdw_refined0.213
r_metal_ion_refined0.193
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.524
r_dihedral_angle_1_deg3.785
r_scangle_it3.449
r_scbond_it2.057
r_mcangle_it1.55
r_angle_refined_deg1.4
r_mcbond_it0.816
r_nbd_refined0.226
r_symmetry_vdw_refined0.213
r_metal_ion_refined0.193
r_xyhbond_nbd_refined0.139
r_symmetry_hbond_refined0.127
r_chiral_restr0.083
r_bond_refined_d0.009
r_gen_planes_refined0.004
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 Atoms2604
Nucleic Acid Atoms
Solvent Atoms354
Heterogen Atoms186

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
AUTOMARdata reduction
AMoREphasing