2DOJ

Crystal structure of the complex of C-terminal lobe of bovine lactoferrin with adenosine at 2.4 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2B6D 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52980.1M MES, PEG, MONOMETHYLETHER, 0.1M ZNSO4 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6653.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.317α = 90
b = 50.465β = 107.66
c = 65.919γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray291IMAGE PLATEMAR scanner 345 mm plate2006-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU300

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
12.463.2597.61535215352
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4399.6

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2B6D2.420153521457776797.420.20.193870.192380.22267RANDOM29.55
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]
-0.29-1.26-0.18-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.277
r_dihedral_angle_1_deg5.284
r_scangle_it3.748
r_scbond_it2.168
r_angle_refined_deg1.945
r_mcangle_it1.561
r_mcbond_it0.825
r_nbd_refined0.248
r_symmetry_vdw_refined0.234
r_symmetry_hbond_refined0.195
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.277
r_dihedral_angle_1_deg5.284
r_scangle_it3.748
r_scbond_it2.168
r_angle_refined_deg1.945
r_mcangle_it1.561
r_mcbond_it0.825
r_nbd_refined0.248
r_symmetry_vdw_refined0.234
r_symmetry_hbond_refined0.195
r_xyhbond_nbd_refined0.176
r_chiral_restr0.125
r_metal_ion_refined0.086
r_bond_refined_d0.013
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2605
Nucleic Acid Atoms
Solvent Atoms230
Heterogen Atoms170

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing