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 Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 298.0
Details 0.1M MES, 25% POLY ETHYLENE GLYCOL MONOMETHYL ETHER-550, 0.1M ZNSO4, PH6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61.43 α = 90
b = 49.87 β = 107.1
c = 65.17 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 203
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate -- 2005-09-06
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8 EMBL/DESY, HAMBURG X13

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.4 62.26 99.6 -- -- -- -- 74524 70446 0.0 0.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.4 1.43 100.0 -- -- -- -- --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.4 62.26 0.0 0.0 74524 70446 3738 99.6 -- 0.204 0.193 0.219 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.4 1.44 -- 262 5133 0.291 0.298 -- 97.86
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.61
Anisotropic B[1][1] 0.7
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.53
Anisotropic B[2][2] -0.63
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.38
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 1.223
r_angle_refined_deg 1.467
r_dihedral_angle_3_deg 13.736
r_mcbond_it 0.635
r_dihedral_angle_4_deg 16.983
r_chiral_restr 0.078
r_scbond_it 1.681
r_dihedral_angle_1_deg 5.216
r_dihedral_angle_2_deg 38.734
r_bond_refined_d 0.006
r_scangle_it 2.829
r_gen_planes_refined 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2605
Nucleic Acid Atoms 0
Heterogen Atoms 200
Solvent Atoms 509

Software

Software
Software Name Purpose
HKL-2000 data collection
AMoRE phasing
REFMAC refinement version: 5.4.0077
DENZO data reduction
SCALEPACK data scaling