1SDX

Crystal structure of the zinc saturated C-terminal half of bovine lactoferrin at 2.0 A resolution reveals two additional zinc binding sites


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP42980.1M MES, 25% polyethylene glycol monomethylether 550, 0.01M zinc sulphate heptahydrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.7154.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.21α = 90
b = 50.57β = 107.64
c = 66.17γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray283IMAGE PLATEMARRESEARCHMirror2004-01-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (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
12.0620910.07914.72489624896
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.062.1750.3152.2

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 REPLACEMENTTHROUGHOUT1NKX2.0619.92489624896108789.90.1920.1920.21RANDOM40.1
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]
7.81-3.82-2.91-4.9
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.9
c_scangle_it4.36
c_mcangle_it3.28
c_scbond_it3.07
c_mcbond_it2.17
c_angle_deg2.1
c_improper_angle_d1.22
c_bond_d0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2594
Nucleic Acid Atoms
Solvent Atoms228
Heterogen Atoms151

Software

Software
Software NamePurpose
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing