3IB0

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 diclofenac


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52980.1M MES, 25% POLY ETHYLENE GLYCOL MONOMETHYL ETHER-550, 0.1M ZNSO4, PH6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties
Matthew coefficientSolvent content
2.5351.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.432α = 90
b = 49.865β = 107.1
c = 65.165γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray203IMAGE PLATEMAR scanner 345 mm plate2005-09-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8EMBL/DESY, HAMBURGX13

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
11.462.2699.67452470446
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.43100

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 1NKX1.462.267452470446373899.60.2040.1930.219RANDOM23.61
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]
0.7-0.53-0.63-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.734
r_dihedral_angle_4_deg16.983
r_dihedral_angle_3_deg13.736
r_dihedral_angle_1_deg5.216
r_scangle_it2.829
r_scbond_it1.681
r_angle_refined_deg1.467
r_mcangle_it1.223
r_mcbond_it0.635
r_chiral_restr0.078
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.734
r_dihedral_angle_4_deg16.983
r_dihedral_angle_3_deg13.736
r_dihedral_angle_1_deg5.216
r_scangle_it2.829
r_scbond_it1.681
r_angle_refined_deg1.467
r_mcangle_it1.223
r_mcbond_it0.635
r_chiral_restr0.078
r_gen_planes_refined0.006
r_bond_refined_d0.006
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_bond_other_d
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_sphericity_bonded
r_mcbond_other
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2605
Nucleic Acid Atoms
Solvent Atoms509
Heterogen Atoms200

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling