4OQO

Crystal structure of the tryptic generated iron-free C-lobe of bovine Lactoferrin at 2.42 Angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3TAJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP42988% Tacsimate, 20% PEG 3350, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.448.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.81α = 90
b = 49.44β = 94.33
c = 97.86γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHMirror2013-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97ESRFBM14

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
12.4297.5899.10.0976.82769127691
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)
12.422.4897.90.243.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3TAJ2.4238.6726291138698.730.224730.222880.25988RANDOM29.707
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]
-0.790.59-0.190.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.881
r_dihedral_angle_4_deg25.307
r_dihedral_angle_3_deg24.133
r_dihedral_angle_1_deg7.907
r_long_range_B_refined6.884
r_long_range_B_other6.883
r_scangle_other4.084
r_mcangle_it3.957
r_mcangle_other3.956
r_angle_other_deg3.769
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.881
r_dihedral_angle_4_deg25.307
r_dihedral_angle_3_deg24.133
r_dihedral_angle_1_deg7.907
r_long_range_B_refined6.884
r_long_range_B_other6.883
r_scangle_other4.084
r_mcangle_it3.957
r_mcangle_other3.956
r_angle_other_deg3.769
r_scbond_it2.504
r_scbond_other2.504
r_mcbond_it2.413
r_mcbond_other2.413
r_angle_refined_deg1.922
r_chiral_restr0.118
r_bond_refined_d0.017
r_gen_planes_other0.009
r_gen_planes_refined0.008
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5316
Nucleic Acid Atoms
Solvent Atoms310
Heterogen Atoms70

Software

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