3IAZ

Structural basis of the prevention of NSAID-induced damage of the gastrointestinal tract by C-terminal half (C-lobe) of bovine colostrum protein lactoferrin: Binding and structural studies of the C-lobe complex with aspirin


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529825% PEG MONOMETHYL ETHER-550, 0.1M ZNSO4, 0.1M MES, PH6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties
Matthews coefficientSolvent content
2.6753.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.308α = 90
b = 50.469β = 107.7
c = 65.942γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray291IMAGE PLATEMAR scanner 345 mm plateMIRROR2006-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54

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
1263.2596.12706724688
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0695.2

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 1NKX263.2527067246881303960.1840.1820.228RANDOM33.65
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]
1.05-1.53-0.8-1.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.909
r_dihedral_angle_1_deg5.387
r_scangle_it4.276
r_scbond_it2.441
r_angle_refined_deg1.739
r_mcangle_it1.681
r_mcbond_it0.888
r_symmetry_hbond_refined0.393
r_nbd_refined0.241
r_symmetry_vdw_refined0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.909
r_dihedral_angle_1_deg5.387
r_scangle_it4.276
r_scbond_it2.441
r_angle_refined_deg1.739
r_mcangle_it1.681
r_mcbond_it0.888
r_symmetry_hbond_refined0.393
r_nbd_refined0.241
r_symmetry_vdw_refined0.23
r_metal_ion_refined0.225
r_xyhbond_nbd_refined0.173
r_chiral_restr0.163
r_bond_refined_d0.011
r_gen_planes_refined0.008
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 Atoms259
Heterogen Atoms189

Software

Software
Software NamePurpose
MAR345dtbdata collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling