3IB1

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 C-lobe complex with indomethacin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529825% PEG MONOMETHYL ETHER-550, 0.1M MES, 0.01M ZNSO4, PH6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties
Matthew coefficientSolvent content
2.7154.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.839α = 90
b = 50.654β = 107.56
c = 66.119γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray291IMAGE PLATEMAR scanner 345 mm plateMIRROR2005-08-01MSINGLE 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
12.262.99912043017853
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.393

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 1NKX2.262.992043017853952910.2120.2090.244RANDOM39.4
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]
2.51-0.53-1.26-1.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg20.429
r_dihedral_angle_1_deg5.708
r_scangle_it4.414
r_scbond_it2.626
r_angle_refined_deg2.231
r_mcangle_it1.927
r_mcbond_it1.046
r_symmetry_vdw_refined0.483
r_metal_ion_refined0.291
r_nbd_refined0.258
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg20.429
r_dihedral_angle_1_deg5.708
r_scangle_it4.414
r_scbond_it2.626
r_angle_refined_deg2.231
r_mcangle_it1.927
r_mcbond_it1.046
r_symmetry_vdw_refined0.483
r_metal_ion_refined0.291
r_nbd_refined0.258
r_symmetry_hbond_refined0.206
r_chiral_restr0.202
r_xyhbond_nbd_refined0.19
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_dihedral_angle_4_deg
r_bond_other_d
r_sphericity_bonded
r_metal_ion_other
r_dihedral_angle_2_deg
r_symmetry_vdw_other
r_gen_planes_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_angle_other_deg
r_mcbond_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2604
Nucleic Acid Atoms
Solvent Atoms244
Heterogen Atoms162

Software

Software
Software NamePurpose
MAR345dtbdata collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling